GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcB in Pseudomonas fluorescens FW300-N2E2

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate Pf6N2E2_4752 Malate synthase G (EC 2.3.3.9)

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



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 Malate synthase G (EC
           2.3.3.9)
          Length = 725

 Score = 1230 bits (3183), Expect = 0.0
 Identities = 596/726 (82%), Positives = 665/726 (91%), Gaps = 1/726 (0%)

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

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           QA+IDAWHQAR GQAHDAVAYK+FLQ+IGYLLPEA DFQATT+NVD+EIARMAGPQLVVP
Sbjct: 61  QARIDAWHQARTGQAHDAVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVP 120

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

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL  GSHVDS  Y+I  GKLVV+LK GS +GL++ AQL GFQG+ASAP  VLLK+NG+HF
Sbjct: 181 PLAAGSHVDSIAYKIVDGKLVVTLKGGSNSGLRDDAQLIGFQGDASAPTTVLLKHNGLHF 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+  +TLHGRSLLF+RNVGHLMT DAILD+ GNEV
Sbjct: 301 AEEVAKGGQTFTRTMNPDRVYTAVDGSS-VTLHGRSLLFVRNVGHLMTIDAILDQHGNEV 359

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEGI+DGL TSL A+H+LNGNTSR+N+RTGS+YIVKPKMHGPEE AF  ELFGRVEDVL 
Sbjct: 360 PEGILDGLITSLAAIHSLNGNTSRRNSRTGSVYIVKPKMHGPEEAAFTNELFGRVEDVLN 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 LKRMAPVVDRQNASDPLYRPLAPDFDRNIAFQAAVELVIEGTKQPNGYTEPVLHRRRREF 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: 1643
Number of extensions: 52
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 Pf6N2E2_4752 (Malate synthase G (EC 2.3.3.9))
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.20253.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 1209.6   1.2          0 1209.4   1.2    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752  Malate synthase G (EC 2.3.3.9)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752  Malate synthase G (EC 2.3.3.9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1209.4   1.2         0         0       2     720 ..       4     722 ..       3     723 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1209.4 bits;  conditional E-value: 0
                                      TIGR01345   2 rvdagrlqvakklkdfveeevlpgtgvdaekfwsgfdeivrdlapenrellakrdeiqaaidey 65 
                                                    +v++g+lqvak+l dfv++e++pgtg+ a++fw+g d++++dlap+n+ llakrd++qa id++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752   4 HVQVGGLQVAKVLFDFVNNEAIPGTGLTADAFWAGADKVIHDLAPKNKALLAKRDDFQARIDAW 67 
                                                    6899************************************************************ PP

                                      TIGR01345  66 hrknk.gvidkeayksflkeigylveepervtietenvdseiasqagpqlvvpvlnaryalnaa 128
                                                    h+  +  + d  ayk fl++igyl +e    + +t+nvd+eia  agpqlvvpv+nar+alna+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752  68 HQARTgQAHDAVAYKAFLQDIGYLLPEAADFQATTQNVDDEIARMAGPQLVVPVMNARFALNAS 131
                                                    ***99557899***************************************************** PP

                                      TIGR01345 129 narwgslydalygsnvipeedgaekgkeynpkrgekviefarefldeslplesgsyadvvkyki 192
                                                    narwgslydalyg+++i+e dgaekgk yn +rg+kvi+far flde+ pl +gs+ d ++yki
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 132 NARWGSLYDALYGTDAISEADGAEKGKGYNKVRGDKVIAFARAFLDEAAPLAAGSHVDSIAYKI 195
                                                    **************************************************************** PP

                                      TIGR01345 193 vdkklavqlesgkvtrlkdeeqfvgyrgdaadpevillktnglhielqidarhpigkadkakvk 256
                                                    vd+kl+v+l+ g+   l+d++q +g++gda++p+++llk+nglh e+qida  p+g++d a+vk
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 196 VDGKLVVTLKGGSNSGLRDDAQLIGFQGDASAPTTVLLKHNGLHFEIQIDASTPVGQTDAAGVK 259
                                                    **************************************************************** PP

                                      TIGR01345 257 divlesaittildcedsvaavdaedkvlvyrnllglmkgtlkeklekngriikrklnedrsyta 320
                                                    di++e+a+tti+dcedsvaavda+dkv++yrn+lglmkg+l e++ k g++++r +n dr+yta
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 260 DILMEAALTTIMDCEDSVAAVDADDKVVIYRNWLGLMKGDLAEEVAKGGQTFTRTMNPDRVYTA 323
                                                    **************************************************************** PP

                                      TIGR01345 321 angeelslhgrsllfvrnvghlmtipviltdegeeipegildgvltsvialydlkvqnklrnsr 384
                                                     +g+ ++lhgrsllfvrnvghlmti +il+++g+e+pegildg++ts+ a++ l+ + + rnsr
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 324 VDGSSVTLHGRSLLFVRNVGHLMTIDAILDQHGNEVPEGILDGLITSLAAIHSLNGNTSRRNSR 387
                                                    **************************************************************** PP

                                      TIGR01345 385 kgsvyivkpkmhgpeevafanklftriedllglerhtlkvgvmdeerrtslnlkaciakvkerv 448
                                                    +gsvyivkpkmhgpee af+n+lf+r+ed+l+l+r+tlkvg+mdeerrt++nlkaci+ + erv
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 388 TGSVYIVKPKMHGPEEAAFTNELFGRVEDVLNLPRNTLKVGIMDEERRTTVNLKACIKAASERV 451
                                                    **************************************************************** PP

                                      TIGR01345 449 afintgfldrtgdeihtsmeagamvrkadmksapwlkayernnvaagltcglrgkaqigkgmwa 512
                                                    +fintgfldrtgdeihtsmeag+mvrkadmk+  w+ aye+ nv+ gl +gl+g+aqigkgmwa
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 452 VFINTGFLDRTGDEIHTSMEAGPMVRKADMKAEKWIGAYENWNVDIGLSTGLQGRAQIGKGMWA 515
                                                    **************************************************************** PP

                                      TIGR01345 513 mpdlmaemlekkgdqlragantawvpsptaatlhalhyhrvdvqkvqkeladaerraelkeilt 576
                                                    mpdlma mle+k+  + agantawvpsptaa+lhalhyh+vdv++ q+ela+   ra+ ++ilt
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 516 MPDLMAAMLEQKIAHPLAGANTAWVPSPTAAALHALHYHKVDVFARQAELAKR-ARASVDDILT 578
                                                    ***************************************************99.899******* PP

                                      TIGR01345 577 ipvaentnwseeeikeeldnnvqgilgyvvrwveqgigcskvpdihnvalmedratlrissqhl 640
                                                    ip+a n nw+ e+ik+eldnn+qgilgyvvrw++qg+gcskvpdi ++ lmedratlrissqh+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 579 IPLAVNPNWTPEQIKNELDNNAQGILGYVVRWIDQGVGCSKVPDINDIGLMEDRATLRISSQHI 642
                                                    **************************************************************** PP

                                      TIGR01345 641 anwlrhgivskeqvleslermakvvdkqnagdeayrpmadnleasvafkaakdlilkgtkqpsg 704
                                                    anwlrhgiv+++qv+esl+rma vvd+qna d+ yrp+a+++++ +af+aa +l+++gtkqp+g
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 643 ANWLRHGIVTQDQVMESLKRMAPVVDRQNASDPLYRPLAPDFDRNIAFQAAVELVIEGTKQPNG 706
                                                    **************************************************************** PP

                                      TIGR01345 705 ytepilharrlefkek 720
                                                    ytep+lh+rr+efk+ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4752 707 YTEPVLHRRRREFKAA 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 12.33
//
[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 paper from 2022 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