GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_068170823.1 HTA01S_RS10480 4-aminobutyrate--2-oxoglutarate transaminase

Query= BRENDA::Q0K2K2
         (423 letters)



>NCBI__GCF_001592305.1:WP_068170823.1
          Length = 428

 Score =  548 bits (1412), Expect = e-160
 Identities = 276/419 (65%), Positives = 328/419 (78%), Gaps = 3/419 (0%)

Query: 5   NLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVM 64
           N   +QRR  ATPRGVGVM DF+ D A+NA LWD+EGR + DFA GIAVLNTGH HP+V 
Sbjct: 10  NAAWHQRRLDATPRGVGVMGDFFIDHAKNAELWDIEGRRFIDFAGGIAVLNTGHVHPKVQ 69

Query: 65  QAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIAR 124
            AIAAQL+RFTH+ YQ+VPY  YV+LAERINA+VPI+G  KTA F+TGAEA+ENAIKIAR
Sbjct: 70  AAIAAQLQRFTHSCYQVVPYAEYVSLAERINAIVPIEGKAKTAFFSTGAEAIENAIKIAR 129

Query: 125 AHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERA 184
           + TGR GVIAF GAFHGR+L  ++LTGKV PYK GFGPFP +IYH PFP+   G S +  
Sbjct: 130 SSTGRSGVIAFGGAFHGRSLFAVSLTGKVQPYKAGFGPFPPEIYHVPFPA--EGASLDET 187

Query: 185 LQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQT 244
            +A++ +FK DI+P+RVAAI+ EPVQGEGGF     D +  LRA+CDQHGI+LIADEVQT
Sbjct: 188 KRAMDHVFKCDIEPSRVAAIVFEPVQGEGGFNPIQKDAVLWLRALCDQHGILLIADEVQT 247

Query: 245 GFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPL 304
           GF RTG+MFAM H+ V PDL+TMAKS+AGG  LSAVSG+AAIMD P PGGLGGTYAGNPL
Sbjct: 248 GFARTGRMFAMEHYGVSPDLMTMAKSMAGGTTLSAVSGKAAIMDGPAPGGLGGTYAGNPL 307

Query: 305 AVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPA 364
           A+AA+HAV+DV+ EEKL ER+  LG QL  HL A +   P + EVRGLG+MVA EF D A
Sbjct: 308 AIAASHAVLDVMAEEKLPERAQRLGDQLVAHLRAAKAKYPRIGEVRGLGAMVACEFVD-A 366

Query: 365 TGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALAE 423
            G P A+  K+VQ  AL+ GL+LLTCG YGNVIR+L+PLTI  + F  AL VL  A+AE
Sbjct: 367 AGAPDADTTKQVQAAALKRGLLLLTCGVYGNVIRYLFPLTIEDSVFAEALGVLDAAMAE 425


Lambda     K      H
   0.321    0.136    0.400 

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: 627
Number of extensions: 23
Number of successful extensions: 3
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: 423
Length of database: 428
Length adjustment: 32
Effective length of query: 391
Effective length of database: 396
Effective search space:   154836
Effective search space used:   154836
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 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate WP_068170823.1 HTA01S_RS10480 (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.739983.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-176  573.1   2.5   1.7e-176  572.9   2.5    1.0  1  NCBI__GCF_001592305.1:WP_068170823.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001592305.1:WP_068170823.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.9   2.5  1.7e-176  1.7e-176       1     419 [.      15     424 ..      15     425 .. 0.98

  Alignments for each domain:
  == domain 1  score: 572.9 bits;  conditional E-value: 1.7e-176
                             TIGR00700   1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvv 73 
                                           qrr+ a+++Gvgv+ ++++ +a++ael d++G+r+id+a+giavln+Gh hPkv +a+  q++++th+++qvv
  NCBI__GCF_001592305.1:WP_068170823.1  15 QRRLDATPRGVGVMGDFFIDHAKNAELWDIEGRRFIDFAGGIAVLNTGHVHPKVQAAIAAQLQRFTHSCYQVV 87 
                                           89*********************************************************************** PP

                             TIGR00700  74 pyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkP 146
                                           py  yv+lae++nai P  g++k++++++Gaea+ena+kiar+ tgr gv+af ++fhGr+ ++++lt+kv+P
  NCBI__GCF_001592305.1:WP_068170823.1  88 PYAEYVSLAERINAIVPIEGKAKTAFFSTGAEAIENAIKIARSSTGRSGVIAFGGAFHGRSLFAVSLTGKVQP 160
                                           ************************************************************************* PP

                             TIGR00700 147 ykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakel 219
                                           yk GfGPf+pe+y++P+p +          sld+  +a++++f+ d+e+ +vaa+v+ePvqGeGGf+   k+ 
  NCBI__GCF_001592305.1:WP_068170823.1 161 YKAGFGPFPPEIYHVPFPAE--------GASLDETKRAMDHVFKCDIEPSRVAAIVFEPVQGEGGFNPIQKDA 225
                                           *****************975........245677778************************************ PP

                             TIGR00700 220 vaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGgl 292
                                           v  ++ lc++hgi+liadevqtGfartG++fa+eh+++ Pdl+t+aks+a+G  ls+v G+a i+d papGgl
  NCBI__GCF_001592305.1:WP_068170823.1 226 VLWLRALCDQHGILLIADEVQTGFARTGRMFAMEHYGVSPDLMTMAKSMAGGTTLSAVSGKAAIMDGPAPGGL 298
                                           ************************************************************************* PP

                             TIGR00700 293 GGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdtteP 365
                                           GGtyaGnPla+aa++avld++ ee l era+++g  +  +l  +k++ p+ig+vrglGam+a e+vd+ ++ P
  NCBI__GCF_001592305.1:WP_068170823.1 299 GGTYAGNPLAIAASHAVLDVMAEEKLPERAQRLGDQLVAHLRAAKAKYPRIGEVRGLGAMVACEFVDA-AGAP 370
                                           ******************************************************************97.578* PP

                             TIGR00700 366 daalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                           da  +++++aaal++Gllllt+G++Gn+ir+l Plti d+ + e+l +l aa+a
  NCBI__GCF_001592305.1:WP_068170823.1 371 DADTTKQVQAAALKRGLLLLTCGVYGNVIRYLFPLTIEDSVFAEALGVLDAAMA 424
                                           **************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (428 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: 15.24
//
[ok]

This GapMind analysis is from Apr 09 2024. 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