GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Chlorobium phaeobacteroides BS1

Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate 642684930 Cphamn1_2453 adenosylmethionine-8-amino-7-oxononanoate aminotransferase apoenzyme (EC 2.6.1.62)

Query= uniprot:A1S8Y2
         (425 letters)



>IMG__ChlphaBS1_FD:642684930
          Length = 434

 Score =  165 bits (417), Expect = 3e-45
 Identities = 124/357 (34%), Positives = 176/357 (49%), Gaps = 31/357 (8%)

Query: 25  PVFTERAENATVWDVE-GREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEKFSHTCFMVLG 83
           PV+  +  +    ++E GR  ID          G+ HP +  AV +QLEK SH  F    
Sbjct: 27  PVYPVKGASGVRIELEDGRRLIDGMSSWWAAIHGYNHPVLNEAVRKQLEKMSHVMFGGFT 86

Query: 84  YESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAIKVARAYTKRAG------VIAFTS 137
           +E  V + EKL  L PG   +K     SGS +VE AIK+A  Y   AG      ++   S
Sbjct: 87  HEPAVRLAEKLVDLTPGPL-QKVFFSDSGSVSVEVAIKMALQYHHAAGRPKKNRLLTIRS 145

Query: 138 GYHGRTMAALALTGKVAP-YSKGMGLMQANVFRAEFPCALHGVSEDDAMASIERIFKNDA 196
           GYHG T AA+++   V   +    G++   +F     C  H V  DD++    R  + + 
Sbjct: 146 GYHGDTFAAMSVCDPVTGMHGLFSGVLPQQLFAEAPACGFHDVWSDDSIGDFRR--QVEM 203

Query: 197 EPSDIAAIILEPV-QGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTGAGRTGTFFAM 255
              +IAA+ILEPV QG GG    +P ++ R+RELCDR  ++LI DE+ TG GRTG  FA+
Sbjct: 204 YHREIAAVILEPVVQGAGGMRFYSPEYLVRVRELCDRYDLLLIFDEIATGFGRTGKMFAL 263

Query: 256 EQMGVAADITTFAKSIAGGF----------PLSGITGRAEVMDAIGPGGL--GGTYGGSP 303
           E   V  DI    K++ GG+           +SG+   AE      PG    G T+  +P
Sbjct: 264 EHADVVPDILCIGKALTGGYMTLAATLTNGDVSGVISNAE------PGVFMHGPTFMANP 317

Query: 304 LACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIEL 360
           LACA A A I++  E         I   + S + E     P +A+VR LG++  +EL
Sbjct: 318 LACAVASASIDLLAESDWRNSVRVIEAQLASGL-EPCRIVPGVADVRVLGAIGVVEL 373


Lambda     K      H
   0.319    0.136    0.391 

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: 421
Number of extensions: 26
Number of successful extensions: 7
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: 434
Length adjustment: 32
Effective length of query: 393
Effective length of database: 402
Effective search space:   157986
Effective search space used:   157986
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)

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