GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Marivita geojedonensis DPG-138

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate WP_085639734.1 MGEO_RS15340 4-aminobutyrate--2-oxoglutarate transaminase

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



>NCBI__GCF_002115805.1:WP_085639734.1
          Length = 460

 Score =  477 bits (1227), Expect = e-139
 Identities = 241/422 (57%), Positives = 307/422 (72%), Gaps = 2/422 (0%)

Query: 5   NASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKII 64
           NA+L  RRE AV RGVG   P+FA  A+NA + DVEG+ +IDFAGGIAVLNTGH HP +I
Sbjct: 28  NAALWARRETAVARGVGSAAPVFAARAENAELWDVEGKRYIDFAGGIAVLNTGHRHPSVI 87

Query: 65  AAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIAR 124
           AA   Q +  THT FQV+ YEPY+ L EK+NA  PGDFAKKTLLVTTG+EAVENAVKIAR
Sbjct: 88  AAAKAQEDLYTHTSFQVVPYEPYIALAEKLNALAPGDFAKKTLLVTTGAEAVENAVKIAR 147

Query: 125 AATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDS 184
           A TGR GVIAFT  YHGRT++TLGLTGKV PY   +G  P  IFRA +P+   G+++ DS
Sbjct: 148 AHTGRPGVIAFTAGYHGRTLLTLGLTGKVNPYKKDVGPFPSDIFRAPFPDTRAGLTVSDS 207

Query: 185 IASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQT 244
           + ++E +F  DA+P  +AAII+EPV GEGG++  P E  + LRA+CD+HGILLI+DE+Q 
Sbjct: 208 LRALETLFLTDAQPDRVAAIILEPVLGEGGYHPVPTEMWQALRAICDKHGILLISDEIQA 267

Query: 245 GAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPI 304
           G  RTGT+FA+E  GV  DL T AKS+AGG+P+AGV G+AE MDA+ PGGLGGTY G+P+
Sbjct: 268 GFARTGTWFAIEHSGVAPDLITCAKSMAGGYPVAGVIGRAEVMDALEPGGLGGTYGGNPV 327

Query: 305 ACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPV--IGEVRALGAMIAVELFE 362
           ACAAALA +E  E E LL R  A+G+ +      I A+     + ++R LGAM+AVE   
Sbjct: 328 ACAAALAAIEAIESEDLLARSTALGDTMRARFADIGARVAPFRMWDIRGLGAMLAVEFVT 387

Query: 363 NGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEECF 422
           +  +  P+ A    V+A A  +GLILLSCG +GN +R++VPLT+ DA +++GLAI E   
Sbjct: 388 DFGTATPDVALTKSVIAHALKRGLILLSCGMHGNAVRIMVPLTASDAIIEEGLAIFEAAL 447

Query: 423 AE 424
           A+
Sbjct: 448 AD 449


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: 614
Number of extensions: 24
Number of successful extensions: 4
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: 460
Length adjustment: 32
Effective length of query: 393
Effective length of database: 428
Effective search space:   168204
Effective search space used:   168204
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_085639734.1 MGEO_RS15340 (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.667423.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-168  546.9   2.3   1.5e-168  546.7   2.3    1.0  1  NCBI__GCF_002115805.1:WP_085639734.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085639734.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  546.7   2.3  1.5e-168  1.5e-168       2     420 .]      34     449 ..      33     449 .. 0.97

  Alignments for each domain:
  == domain 1  score: 546.7 bits;  conditional E-value: 1.5e-168
                             TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 
                                           rr++av++Gvg +++v+aa+ae+ael dv+G+r+id+a+giavln+Gh+hP v++a k q + +tht+fqvvp
  NCBI__GCF_002115805.1:WP_085639734.1  34 RRETAVARGVGSAAPVFAARAENAELWDVEGKRYIDFAGGIAVLNTGHRHPSVIAAAKAQEDLYTHTSFQVVP 106
                                           89*********************************************************************** PP

                             TIGR00700  75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147
                                           ye y++laeklna+aPg   kk++l+++Gaeavenavkiar++tgrpgv+af+ g+hGrt lt+ lt+kv+Py
  NCBI__GCF_002115805.1:WP_085639734.1 107 YEPYIALAEKLNALAPGDFAKKTLLVTTGAEAVENAVKIARAHTGRPGVIAFTAGYHGRTLLTLGLTGKVNPY 179
                                           ************************************************************************* PP

                             TIGR00700 148 kiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelv 220
                                           k   GPf+++++raP+p +   +++     + d l+a+e+lf +d ++++vaa++lePv GeGG+   + e+ 
  NCBI__GCF_002115805.1:WP_085639734.1 180 KKDVGPFPSDIFRAPFPDTRA-GLT-----VSDSLRALETLFLTDAQPDRVAAIILEPVLGEGGYHPVPTEMW 246
                                           *****************7644.444.....456788******************************99***** PP

                             TIGR00700 221 aavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglG 293
                                           +a++ +c++hgi+li+de+q+GfartG+ faieh ++ Pdlit aks+a+G P++gv+Grae++da +pGglG
  NCBI__GCF_002115805.1:WP_085639734.1 247 QALRAICDKHGILLISDEIQAGFARTGTWFAIEHSGVAPDLITCAKSMAGGYPVAGVIGRAEVMDALEPGGLG 319
                                           ************************************************************************* PP

                             TIGR00700 294 GtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevp..aigdvrglGamiavelv.dpdtt 363
                                           Gty+GnP+a+aaala ++ ie+e l  r+  +g  ++ +  ++ + v   ++ d+rglGam+ave+v d +t+
  NCBI__GCF_002115805.1:WP_085639734.1 320 GTYGGNPVACAAALAAIEAIESEDLLARSTALGDTMRARFADIGARVApfRMWDIRGLGAMLAVEFVtDFGTA 392
                                           *****************************************998766434689**************99**** PP

                             TIGR00700 364 ePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaalad 420
                                            Pd al++ + a+al++Gl+ll++G++Gn +r++ Plt sd++++egl i eaalad
  NCBI__GCF_002115805.1:WP_085639734.1 393 TPDVALTKSVIAHALKRGLILLSCGMHGNAVRIMVPLTASDAIIEEGLAIFEAALAD 449
                                           *******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (460 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: 17.50
//
[ok]

This GapMind analysis is from Sep 24 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