GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Pseudomonas stutzeri RCH2

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate GFF3586 Psest_3653 4-aminobutyrate aminotransferase, prokaryotic type

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



>FitnessBrowser__psRCH2:GFF3586
          Length = 426

 Score =  727 bits (1877), Expect = 0.0
 Identities = 366/425 (86%), Positives = 393/425 (92%)

Query: 1   MSKTNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60
           MSKTN SLM+RR AAVPRGVGQIHPIFAD AKN++V DVEGREFIDFAGGIAVLNTGH+H
Sbjct: 1   MSKTNESLMQRRVAAVPRGVGQIHPIFADHAKNSSVVDVEGREFIDFAGGIAVLNTGHLH 60

Query: 61  PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120
           PKII AV +QL+KLTHTCFQVLAYEPYVELCEKINA+VPGDFAKKTLLVTTGSEAVENAV
Sbjct: 61  PKIIKAVEDQLHKLTHTCFQVLAYEPYVELCEKINARVPGDFAKKTLLVTTGSEAVENAV 120

Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180
           KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKV PYSAGMGLMPGGIFRALYP  ++GVS
Sbjct: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVAPYSAGMGLMPGGIFRALYPCAIYGVS 180

Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240
           +DDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGF VAPK+FM RLRALCD+HGILLIAD
Sbjct: 181 VDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFNVAPKDFMARLRALCDEHGILLIAD 240

Query: 241 EVQTGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300
           EVQTGAGRTGTFFAMEQMGV ADLTTFAKS+ GGFP+AGVCGKAE MDAIAPGGLGGTYA
Sbjct: 241 EVQTGAGRTGTFFAMEQMGVVADLTTFAKSVGGGFPIAGVCGKAEIMDAIAPGGLGGTYA 300

Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360
           G+P++CAAALAV+EVFEEE LLDRCKAV ERL TGLKAIQ K+  IGEVR LGAMIA+EL
Sbjct: 301 GNPLSCAAALAVLEVFEEEKLLDRCKAVAERLTTGLKAIQTKHKEIGEVRGLGAMIAIEL 360

Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420
           FE+GD  +P AA  +Q+VA+ARDKGLILLSCGTY NVLRVLVPLT+ D  LD+GLAII E
Sbjct: 361 FEDGDHARPAAALTSQIVARARDKGLILLSCGTYYNVLRVLVPLTAEDELLDRGLAIIGE 420

Query: 421 CFAEL 425
           CF EL
Sbjct: 421 CFDEL 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: 748
Number of extensions: 19
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: 426
Length adjustment: 32
Effective length of query: 393
Effective length of database: 394
Effective search space:   154842
Effective search space used:   154842
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 GFF3586 Psest_3653 (4-aminobutyrate aminotransferase, prokaryotic type)
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.805.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.3e-163  530.4   5.1   1.5e-163  530.2   5.1    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3586  Psest_3653 4-aminobutyrate amino


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3586  Psest_3653 4-aminobutyrate aminotransferase, prokaryotic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.2   5.1  1.5e-163  1.5e-163       1     416 [.      10     420 ..      10     424 .. 0.98

  Alignments for each domain:
  == domain 1  score: 530.2 bits;  conditional E-value: 1.5e-163
                           TIGR00700   1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpy 75 
                                         qrr aav++Gvg   +++a +a+++ + dv+G+++id+a+giavln+Gh hPk+++av+ q+++ltht+fqv+ y
  lcl|FitnessBrowser__psRCH2:GFF3586  10 QRRVAAVPRGVGQIHPIFADHAKNSSVVDVEGREFIDFAGGIAVLNTGHLHPKIIKAVEDQLHKLTHTCFQVLAY 84 
                                         89************************************************************************* PP

                           TIGR00700  76 esyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPykiG 150
                                         e yvel ek+na  Pg   kk++l+++G+eavenavkiar+ tgr gv+af++++hGrt +t+ lt+kv+Py  G
  lcl|FitnessBrowser__psRCH2:GFF3586  85 EPYVELCEKINARVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVAPYSAG 159
                                         *************************************************************************** PP

                           TIGR00700 151 fGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavas 225
                                         +G +++ ++ra +p  + + ++      dd +a+ie++f+ d e++++aa+++ePvqGeGGf+v++k+++a ++ 
  lcl|FitnessBrowser__psRCH2:GFF3586 160 MGLMPGGIFRALYPCAIYGVSV------DDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFNVAPKDFMARLRA 228
                                         **************99887766......88999****************************************** PP

                           TIGR00700 226 lckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnP 300
                                         lc+ehgi+liadevqtG  rtG++fa+e ++++ dl t aks+ +G+P++gv G+aei+da apGglGGtyaGnP
  lcl|FitnessBrowser__psRCH2:GFF3586 229 LCDEHGILLIADEVQTGAGRTGTFFAMEQMGVVADLTTFAKSVGGGFPIAGVCGKAEIMDAIAPGGLGGTYAGNP 303
                                         *************************************************************************** PP

                           TIGR00700 301 lavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekia 374
                                         l++aaalavl++ eee l +r++ + ++++  l  ++ + + ig+vrglGamia+el  d d + P aal+ +i 
  lcl|FitnessBrowser__psRCH2:GFF3586 304 LSCAAALAVLEVFEEEKLLDRCKAVAERLTTGLKAIQTKHKEIGEVRGLGAMIAIELFeDGDHARPAAALTSQIV 378
                                         ********************************************************998999************* PP

                           TIGR00700 375 aaalaaGlllltaGifGniirlltPltisdelldeglkilea 416
                                         a+a+ +Gl+ll++G + n++r+l Plt  delld gl i+ +
  lcl|FitnessBrowser__psRCH2:GFF3586 379 ARARDKGLILLSCGTYYNVLRVLVPLTAEDELLDRGLAIIGE 420
                                         ***************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (426 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.89
//
[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