GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_14100
          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.6498.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: 00:00:00.03
# Mc/sec: 13.13
//
[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:

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