GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Marinobacter adhaerens HP15

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate GFF3766 HP15_3708 4-aminobutyrate aminotransferase

Query= SwissProt::P22256
         (426 letters)



>lcl|FitnessBrowser__Marino:GFF3766 HP15_3708 4-aminobutyrate
           aminotransferase
          Length = 425

 Score =  422 bits (1084), Expect = e-122
 Identities = 210/421 (49%), Positives = 277/421 (65%)

Query: 3   SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62
           SNKEL   + + +  G    +  FAD A N  +WD +G+  +DFAGGI VLN GH HPKV
Sbjct: 2   SNKELQALKERYVAAGAASPNEQFADHATNAELWDADGKRMIDFAGGIGVLNIGHRHPKV 61

Query: 63  VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122
           V AV+AQL KL HTC  V+ YE Y++L E ++  VP     K +L  +G+EA+ENA+KIA
Sbjct: 62  VEAVKAQLDKLMHTCQTVMPYEGYVKLAEKLSGVVPVRGHAKVMLANSGAEALENAMKIA 121

Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182
           RAAT ++  I F G YHGRT YT+A+ GK  PY    G MPG VYRA YP P HG+SED+
Sbjct: 122 RAATGKTNVICFDGGYHGRTFYTMAMNGKAAPYQTDFGPMPGTVYRAPYPVPYHGVSEDE 181

Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242
           A+  +    K D+   + AAIVIEPV GEGGFYA+  +F++ +R +CDE+ I++IADEVQ
Sbjct: 182 ALRGLKMAMKADSPAHNTAAIVIEPVLGEGGFYAAPTSFLKEIRKICDENDILMIADEVQ 241

Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302
           SG GRTG +FA+E  GV PDL T AKS+A G P++ + G  + MDA  P  LGGTY G+P
Sbjct: 242 SGFGRTGKMFAIEHSGVEPDLMTMAKSMADGMPISAIVGTDKYMDASGPNSLGGTYTGSP 301

Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFED 362
            AC AAL V  VF++E++L K+  LG+KLK       E+   + +VR LG M A EL E 
Sbjct: 302 TACAAALAVFDVFKEEDILGKSQALGEKLKQRFSQWQEQFAHVDNVRNLGPMAAFELVES 361

Query: 363 GDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFD 422
            +   P  +L A +  +A++KGLILLSCG Y N LR L+P+TIED  + +GL I+ +   
Sbjct: 362 KESRTPKPELAAAVTKKAKEKGLILLSCGMYGNTLRFLMPVTIEDEVLEEGLAIVEESLK 421

Query: 423 E 423
           E
Sbjct: 422 E 422


Lambda     K      H
   0.320    0.137    0.401 

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: 495
Number of extensions: 15
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: 426
Length of database: 425
Length adjustment: 32
Effective length of query: 394
Effective length of database: 393
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 GFF3766 HP15_3708 (4-aminobutyrate aminotransferase)
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.22916.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.5e-161  522.0   0.6   5.6e-161  521.7   0.6    1.0  1  lcl|FitnessBrowser__Marino:GFF3766  HP15_3708 4-aminobutyrate aminot


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3766  HP15_3708 4-aminobutyrate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.7   0.6  5.6e-161  5.6e-161       5     419 ..      12     421 ..       9     422 .. 0.97

  Alignments for each domain:
  == domain 1  score: 521.7 bits;  conditional E-value: 5.6e-161
                           TIGR00700   5 aavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpyesyv 79 
                                          +v+ G +  ++ +a +a +ael d dG+r+id+a+gi+vln+Gh+hPkvveavk q+++l+ht+ +v+pye+yv
  lcl|FitnessBrowser__Marino:GFF3766  12 RYVAAGAASPNEQFADHATNAELWDADGKRMIDFAGGIGVLNIGHRHPKVVEAVKAQLDKLMHTCQTVMPYEGYV 86 
                                         678999999****************************************************************** PP

                           TIGR00700  80 elaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPykiGfGPf 154
                                         +laekl+++ P+ g++k +l nsGaea+ena+kiar+ tg+  v++f++g+hGrt+ tma+ +k++Py++ fGP+
  lcl|FitnessBrowser__Marino:GFF3766  87 KLAEKLSGVVPVRGHAKVMLANSGAEALENAMKIARAATGKTNVICFDGGYHGRTFYTMAMNGKAAPYQTDFGPM 161
                                         *************************************************************************** PP

                           TIGR00700 155 apevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavaslcke 229
                                         ++ vyraP+p +y++ +   +e+    l+ ++  ++ad  a++ aa+v+ePv GeGGf  ++  ++++++++c+e
  lcl|FitnessBrowser__Marino:GFF3766 162 PGTVYRAPYPVPYHGVSE--DEA----LRGLKMAMKADSPAHNTAAIVIEPVLGEGGFYAAPTSFLKEIRKICDE 230
                                         ***************988..555....5588888999************************************** PP

                           TIGR00700 230 hgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlava 304
                                         ++i++iadevq+Gf rtGk+faieh +++Pdl+t+aks+adG+P+s++vG  + +da+ p  lGGty+G+P a+a
  lcl|FitnessBrowser__Marino:GFF3766 231 NDILMIADEVQSGFGRTGKMFAIEHSGVEPDLMTMAKSMADGMPISAIVGTDKYMDASGPNSLGGTYTGSPTACA 305
                                         *************************************************************************** PP

                           TIGR00700 305 aalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaal 378
                                         aalav+d+ +ee +  +++ +g+ +k++  +++e++  + +vr+lG m+a elv   +++ P+  la++++++a+
  lcl|FitnessBrowser__Marino:GFF3766 306 AALAVFDVFKEEDILGKSQALGEKLKQRFSQWQEQFAHVDNVRNLGPMAAFELVeSKESRTPKPELAAAVTKKAK 380
                                         ******************************************************5557899************** PP

                           TIGR00700 379 aaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                         ++Gl+ll++G++Gn +r+l+P+ti de l+egl i+e++l+
  lcl|FitnessBrowser__Marino:GFF3766 381 EKGLILLSCGMYGNTLRFLMPVTIEDEVLEEGLAIVEESLK 421
                                         *************************************9986 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: 00:00:00.01
# Mc/sec: 9.59
//
[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 preprint 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