GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcB in Pseudomonas fluorescens FW300-N2C3

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate AO356_14100 AO356_14100 malate synthase G

Query= reanno::psRCH2:GFF353
         (726 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100 AO356_14100 malate
           synthase G
          Length = 725

 Score = 1239 bits (3206), Expect = 0.0
 Identities = 601/726 (82%), Positives = 670/726 (92%), Gaps = 1/726 (0%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MTE VQVGGLQVAKVL+DFVNNEAIPGTG+ A AFWAGAD VIHDLAPKN+ALLAKRDD 
Sbjct: 1   MTEHVQVGGLQVAKVLFDFVNNEAIPGTGLTAGAFWAGADKVIHDLAPKNQALLAKRDDF 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           QA+IDAWHQARAGQAHDAVAYK+FLQ+IGYLLPEA DFQATT+NVD+EIARMAGPQLVVP
Sbjct: 61  QARIDAWHQARAGQAHDAVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           +MNARFALNA+NARWGSLYDALYGTDAISEADGA KG GYN++RG+KVIA+AR FL+EAA
Sbjct: 121 VMNARFALNASNARWGSLYDALYGTDAISEADGAEKGKGYNKVRGDKVIAFARAFLDEAA 180

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL  GSHVDST Y+I  GKLVV+LK GS +GL++ AQL GFQG+ASAP AVLLK+NG+HF
Sbjct: 181 PLAAGSHVDSTAYKIVDGKLVVALKGGSNSGLRDDAQLIGFQGDASAPTAVLLKHNGLHF 240

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           EIQID ++P+GQTDAAGVKDILME+ALTTIMDCEDS+AAVDADDK V+YRNWLGLMKGDL
Sbjct: 241 EIQIDASTPVGQTDAAGVKDILMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDL 300

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
            EE+ KGG+  TR MNPDRVYT  DG+G +TLHGRSLLF+RNVGHLMT DAILDK GNEV
Sbjct: 301 SEEVAKGGQTFTRTMNPDRVYTAVDGSG-VTLHGRSLLFVRNVGHLMTIDAILDKHGNEV 359

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEGI+DGL TSL A+H+LNGNTSR+N+RTGS+YIVKPKMHGPEE AF  ELFGRVEDVL 
Sbjct: 360 PEGILDGLVTSLAAIHSLNGNTSRRNSRTGSVYIVKPKMHGPEEAAFTNELFGRVEDVLN 419

Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
           LPRNTLKVGIMDEERRTT+NLKACIK A ERVVFINTGFLDRTGDEIHTSMEAGPMVRKA
Sbjct: 420 LPRNTLKVGIMDEERRTTVNLKACIKAASERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 479

Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
            MKAEKWI AYEN NVD+GL+ GLQG+AQIGKGMWAMPDLMAAMLEQK+ HP+AGANTAW
Sbjct: 480 DMKAEKWIGAYENWNVDIGLSTGLQGRAQIGKGMWAMPDLMAAMLEQKIAHPLAGANTAW 539

Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNN 600
           VPSPTAA LHA+HYHK+DV ARQ ELAKR +AS+DDILTIPLA + NW+ E+ +NELDNN
Sbjct: 540 VPSPTAAALHALHYHKVDVFARQAELAKRARASVDDILTIPLAVNPNWTPEQIKNELDNN 599

Query: 601 SQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVES 660
           +QGILGY+VRW++QGVGCSKVPDINDI LMEDRATLRISSQH+ANW+RHG+VT+DQV+ES
Sbjct: 600 AQGILGYVVRWIDQGVGCSKVPDINDIGLMEDRATLRISSQHIANWLRHGIVTQDQVMES 659

Query: 661 LKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREF 720
           LKRMAPVVDRQN  DPLYRP+APDFD+++AFQAA+ELV+EGTKQPNGYTEPVLHRRRREF
Sbjct: 660 LKRMAPVVDRQNASDPLYRPLAPDFDSNIAFQAAVELVIEGTKQPNGYTEPVLHRRRREF 719

Query: 721 KAKNGL 726
           KA NGL
Sbjct: 720 KAANGL 725


Lambda     K      H
   0.316    0.133    0.386 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1641
Number of extensions: 46
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 726
Length of database: 725
Length adjustment: 40
Effective length of query: 686
Effective length of database: 685
Effective search space:   469910
Effective search space used:   469910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)

Align candidate AO356_14100 AO356_14100 (malate synthase G)
to HMM TIGR01345 (glcB: malate synthase G (EC 2.3.3.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01345.hmm
# target sequence database:        /tmp/gapView.21970.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01345  [M=721]
Accession:   TIGR01345
Description: malate_syn_G: malate synthase G
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
          0 1203.8   0.9          0 1203.6   0.9    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100  AO356_14100 malate synthase G


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100  AO356_14100 malate synthase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1203.6   0.9         0         0       2     720 ..       4     722 ..       3     723 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1203.6 bits;  conditional E-value: 0
                                       TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaide 64 
                                                     +v++g+lqvak+l dfv++e++pgtg+ a +fw+g d++++dlap+n+ llakrd++qa id+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100   4 HVQVGGLQVAKVLFDFVNNEAIPGTGLTAGAFWAGADKVIHDLAPKNQALLAKRDDFQARIDA 66 
                                                     6899*********************************************************** PP

                                       TIGR01345  65 yhrknk.gvidkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryaln 126
                                                     +h+     + d  ayk fl++igyl +e    + +t+nvd+eia  agpqlvvpv+nar+aln
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100  67 WHQARAgQAHDAVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVPVMNARFALN 129
                                                     ****99557899*************************************************** PP

                                       TIGR01345 127 aanarwgslydalygsnvipeedgaekgkeynpkrgekviefarefldeslplesgsyadvvk 189
                                                     a+narwgslydalyg+++i+e dgaekgk yn +rg+kvi+far flde+ pl +gs+ d  +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100 130 ASNARWGSLYDALYGTDAISEADGAEKGKGYNKVRGDKVIAFARAFLDEAAPLAAGSHVDSTA 192
                                                     *************************************************************** PP

                                       TIGR01345 190 ykivdkklavqlesgkvtrlkdeeqfvgyrgdaadpevillktnglhielqidarhpigkadk 252
                                                     ykivd+kl+v l+ g+   l+d++q +g++gda++p+++llk+nglh e+qida  p+g++d 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100 193 YKIVDGKLVVALKGGSNSGLRDDAQLIGFQGDASAPTAVLLKHNGLHFEIQIDASTPVGQTDA 255
                                                     *************************************************************** PP

                                       TIGR01345 253 akvkdivlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekngriikrklned 315
                                                     a+vkdi++e+a+tti+dcedsvaavda+dkv++yrn+lglmkg+l e++ k g++++r +n d
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100 256 AGVKDILMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDLSEEVAKGGQTFTRTMNPD 318
                                                     *************************************************************** PP

                                       TIGR01345 316 rsytaangeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqn 378
                                                     r+yta +g+ ++lhgrsllfvrnvghlmti +il+++g+e+pegildg++ts+ a++ l+ + 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100 319 RVYTAVDGSGVTLHGRSLLFVRNVGHLMTIDAILDKHGNEVPEGILDGLVTSLAAIHSLNGNT 381
                                                     *************************************************************** PP

                                       TIGR01345 379 klrnsrkgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaci 441
                                                     + rnsr+gsvyivkpkmhgpee af+n+lf+r+ed+l+l+r+tlkvg+mdeerrt++nlkaci
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100 382 SRRNSRTGSVYIVKPKMHGPEEAAFTNELFGRVEDVLNLPRNTLKVGIMDEERRTTVNLKACI 444
                                                     *************************************************************** PP

                                       TIGR01345 442 akvkervafintgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgka 504
                                                     + + erv+fintgfldrtgdeihtsmeag+mvrkadmk+  w+ aye+ nv+ gl +gl+g+a
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100 445 KAASERVVFINTGFLDRTGDEIHTSMEAGPMVRKADMKAEKWIGAYENWNVDIGLSTGLQGRA 507
                                                     *************************************************************** PP

                                       TIGR01345 505 qigkgmwampdlmaemlekkgdqlragantawvpsptaatlhalhyhrvdvqkvqkeladaer 567
                                                     qigkgmwampdlma mle+k+  + agantawvpsptaa+lhalhyh+vdv++ q+ela+   
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100 508 QIGKGMWAMPDLMAAMLEQKIAHPLAGANTAWVPSPTAAALHALHYHKVDVFARQAELAKR-A 569
                                                     ***********************************************************99.8 PP

                                       TIGR01345 568 raelkeiltipvaentnwseeeikeeldnnvqgilgyvvrwveqgigcskvpdihnvalmedr 630
                                                     ra+ ++iltip+a n nw+ e+ik+eldnn+qgilgyvvrw++qg+gcskvpdi ++ lmedr
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100 570 RASVDDILTIPLAVNPNWTPEQIKNELDNNAQGILGYVVRWIDQGVGCSKVPDINDIGLMEDR 632
                                                     99************************************************************* PP

                                       TIGR01345 631 atlrissqhlanwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleasvafkaakd 693
                                                     atlrissqh+anwlrhgiv+++qv+esl+rma vvd+qna d+ yrp+a+++++ +af+aa +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100 633 ATLRISSQHIANWLRHGIVTQDQVMESLKRMAPVVDRQNASDPLYRPLAPDFDSNIAFQAAVE 695
                                                     *************************************************************** PP

                                       TIGR01345 694 lilkgtkqpsgytepilharrlefkek 720
                                                     l+++gtkqp+gytep+lh+rr+efk+ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_14100 696 LVIEGTKQPNGYTEPVLHRRRREFKAA 722
                                                     *************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (721 nodes)
Target sequences:                          1  (725 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.05
# Mc/sec: 10.19
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory