Alignments for a candidate for gabT in Marinomonas arctica 328

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Marinomonas arctica 328

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate WP_111605742.1 DK187_RS02410 4-aminobutyrate--2-oxoglutarate transaminase

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



>NCBI__GCF_003259225.1:WP_111605742.1
          Length = 425

 Score =  458 bits (1179), Expect = e-133
 Identities = 231/422 (54%), Positives = 288/422 (68%), Gaps = 1/422 (0%)

Query: 5   NASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKII 64
           NA + KR+E+A+ RG   + P++ D A NA + DVEG+ +IDF  GIAV+NTGH HPK+ 
Sbjct: 3   NADIQKRKESAIARGQANMAPVYVDRALNAEIWDVEGKRYIDFGAGIAVVNTGHNHPKVK 62

Query: 65  AAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIAR 124
           AA   Q+ + THTC  V  YE  V L EK+NA  PG+  KK++ VTTG+EAVEN VKIAR
Sbjct: 63  AATIAQIERFTHTCVMVSPYESAVALAEKLNAAAPGNTPKKSIFVTTGAEAVENCVKIAR 122

Query: 125 AATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDS 184
           A TGR G+IAF G YHGRT MT+GLTGKV PY  G G  P  IF   YPN+  G++ + +
Sbjct: 123 AHTGRPGIIAFNGGYHGRTNMTMGLTGKVNPYKIGFGPFPSDIFHVPYPNDYLGITEEQA 182

Query: 185 IASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQT 244
           +A ++  F  D EP  +AAIIIEPVQGEGGFY A   F+++LR LCD HG+LLI DE+Q+
Sbjct: 183 LADLQLRFTCDIEPSRVAAIIIEPVQGEGGFYKASTSFLQKLRKLCDDHGMLLILDEIQS 242

Query: 245 GAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPI 304
           G  RTGT F  EQ G+ ADL T AK IAGG PLA V GKA  MDA  PGGLGGTY GSP+
Sbjct: 243 GFARTGTMFCHEQAGIEADLMTTAKGIAGGVPLAAVVGKANIMDAPIPGGLGGTYGGSPV 302

Query: 305 ACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYP-VIGEVRALGAMIAVELFEN 363
            CAA LAV EV EEE L +R   +G R V  L A+QA++P +IG+VR  GAMIAVE   +
Sbjct: 303 GCAAGLAVFEVIEEEKLCERATQIGTRFVEHLTALQAEFPNIIGDVRNSGAMIAVEFVHD 362

Query: 364 GDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEECFA 423
           GD +KP      ++  KA + GL+LLSCG  GNV+R L  LT     +D+G+ I ++CF 
Sbjct: 363 GDVNKPYPELAKKLSGKASENGLVLLSCGIRGNVIRFLPALTIEMELIDEGMEIFKDCFK 422

Query: 424 EL 425
            L
Sbjct: 423 AL 424


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: 557
Number of extensions: 20
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: 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 WP_111605742.1 DK187_RS02410 (4-aminobutyrate--2-oxoglutarate transaminase)
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.911340.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.8e-174  563.7   1.6   1.1e-173  563.6   1.6    1.0  1  NCBI__GCF_003259225.1:WP_111605742.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003259225.1:WP_111605742.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  563.6   1.6  1.1e-173  1.1e-173       1     418 [.       8     421 ..       7     423 .. 0.97

  Alignments for each domain:
  == domain 1  score: 563.6 bits;  conditional E-value: 1.1e-173
                             TIGR00700   1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvv 73 
                                           +r+++a+++G +++++v++ +a +ae+ dv+G+r+id++agiav+n+Gh+hPkv +a   q+e++tht+ +v 
  NCBI__GCF_003259225.1:WP_111605742.1   8 KRKESAIARGQANMAPVYVDRALNAEIWDVEGKRYIDFGAGIAVVNTGHNHPKVKAATIAQIERFTHTCVMVS 80 
                                           47789******************************************************************** PP

                             TIGR00700  74 pyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkP 146
                                           pyes v+laeklna aPg  +kk++++++Gaeaven vkiar++tgrpg++af++g+hGrtn+tm lt+kv+P
  NCBI__GCF_003259225.1:WP_111605742.1  81 PYESAVALAEKLNAAAPGNTPKKSIFVTTGAEAVENCVKIARAHTGRPGIIAFNGGYHGRTNMTMGLTGKVNP 153
                                           ************************************************************************* PP

                             TIGR00700 147 ykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakel 219
                                           ykiGfGPf+++++++P+p dy +i+   +++    la ++  f  d+e+ +vaa+++ePvqGeGGf  ++  +
  NCBI__GCF_003259225.1:WP_111605742.1 154 YKIGFGPFPSDIFHVPYPNDYLGITE--EQA----LADLQLRFTCDIEPSRVAAIIIEPVQGEGGFYKASTSF 220
                                           **********************9988..333....44577789****************************** PP

                             TIGR00700 220 vaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGgl 292
                                           ++++++lc++hg++li de+q+GfartG++f  e  + + dl+t+ak++a+G+Pl++vvG+a+i+dap pGgl
  NCBI__GCF_003259225.1:WP_111605742.1 221 LQKLRKLCDDHGMLLILDEIQSGFARTGTMFCHEQAGIEADLMTTAKGIAGGVPLAAVVGKANIMDAPIPGGL 293
                                           ************************************************************************* PP

                             TIGR00700 293 GGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpa.igdvrglGamiavelv.dpdtt 363
                                           GGty+G+P+++aa lav+++ieee l+era qig +  ++l+ l++e+p  igdvr+ Gamiave+v d d +
  NCBI__GCF_003259225.1:WP_111605742.1 294 GGTYGGSPVGCAAGLAVFEVIEEEKLCERATQIGTRFVEHLTALQAEFPNiIGDVRNSGAMIAVEFVhDGDVN 366
                                           ************************************************9637***************999*** PP

                             TIGR00700 364 ePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaal 418
                                           +P   la+k++ +a ++Gl+ll++Gi Gn+ir+l+ lti  el+deg++i ++ +
  NCBI__GCF_003259225.1:WP_111605742.1 367 KPYPELAKKLSGKASENGLVLLSCGIRGNVIRFLPALTIEMELIDEGMEIFKDCF 421
                                           **************************************************99976 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 16.25
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources