GapMind for catabolism of small carbon sources

 

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

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate Pf6N2E2_4013 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= metacyc::MONOMER-11537
         (425 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 5-aminovalerate
           aminotransferase (EC 2.6.1.48) /
           Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase
           (EC 2.6.1.19)
          Length = 425

 Score =  815 bits (2106), Expect = 0.0
 Identities = 413/425 (97%), Positives = 418/425 (98%)

Query: 1   MSKTNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60
           MSKTNA LM RR AAVPRGVGQIHPIFA+SAKNATVTDVEGREFIDFAGGIAVLNTGHVH
Sbjct: 1   MSKTNADLMARRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60

Query: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120
           PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV
Sbjct: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120

Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180
           KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS
Sbjct: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180

Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240
           IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD
Sbjct: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240

Query: 241 EVQTGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300
           EVQTGAGRTGTFFAMEQMGV ADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA
Sbjct: 241 EVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300

Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360
           GSPIACAAALAVMEVFEEEHLLDRCKAVGERLV GLKAIQ KYPVIG+VRALGAMIAVEL
Sbjct: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGAMIAVEL 360

Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420
           FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLT+PD QLDKGLAI+EE
Sbjct: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAILEE 420

Query: 421 CFAEL 425
           CF+EL
Sbjct: 421 CFSEL 425


Lambda     K      H
   0.320    0.137    0.394 

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: 814
Number of extensions: 21
Number of successful extensions: 1
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: 425
Length of database: 425
Length adjustment: 32
Effective length of query: 393
Effective length of database: 393
Effective search space:   154449
Effective search space used:   154449
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate Pf6N2E2_4013 (5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19))
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

# 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/TIGR00700.hmm
# target sequence database:        /tmp/gapView.15921.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00700  [M=420]
Accession:   TIGR00700
Description: GABAtrnsam: 4-aminobutyrate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   3.2e-167  542.3   7.3   3.7e-167  542.1   7.3    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013  5-aminovalerate aminotransferase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013  5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.1   7.3  3.7e-167  3.7e-167       2     418 ..      11     422 ..      10     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 542.1 bits;  conditional E-value: 3.7e-167
                                      TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveel 65 
                                                    rr+aav++Gvg   +++a +a++a++ dv+G+++id+a+giavln+Gh hPk+++av +q+++l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013  11 RRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKL 74 
                                                    89************************************************************** PP

                                      TIGR00700  66 thtafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrg 129
                                                    tht+fqv+ ye yvel ek+na  Pg   kk++l+++G+eavenavkiar+ tgr gv+af+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013  75 THTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGA 138
                                                    **************************************************************** PP

                                      TIGR00700 130 fhGrtnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadv 193
                                                    +hGrt +t+ lt+kv Py  G+G +++ ++ra +p ++++ +       dd +a+ie++f+ d 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSI------DDSIASIERIFKNDA 196
                                                    ***************************************9877......88899********** PP

                                      TIGR00700 194 eaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaiehedd 257
                                                    e++++aa+++ePvqGeGGf v++ke+++ ++ lc++hgi+liadevqtG  rtG++fa+e +++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 197 EPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGV 260
                                                    **************************************************************** PP

                                      TIGR00700 258 kPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieeeglier 321
                                                      dl t aks+a+G+Pl+gv G+ae +da apGglGGtyaG+P+a+aaalav+++ eee l +r
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 261 AADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHLLDR 324
                                                    **************************************************************** PP

                                      TIGR00700 322 aeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaalaaGlll 384
                                                    ++ +g+++   l  ++++ p+igdvr lGamiavel  + d+++P+aa  +++ a+a+ +Gl+l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 325 CKAVGERLVAGLKAIQKKYPVIGDVRALGAMIAVELFeNGDSHKPNAAAVAQVVAKARDKGLIL 388
                                                    ***********************************9968899********************** PP

                                      TIGR00700 385 ltaGifGniirlltPltisdelldeglkileaal 418
                                                    l++G +Gn++r+l Plt +de+ld+gl ile+ +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 389 LSCGTYGNVLRVLVPLTAPDEQLDKGLAILEECF 422
                                                    ******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (425 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.04
//
[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