GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Chlorobium phaeobacteroides BS1

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 642684930 Cphamn1_2453 adenosylmethionine-8-amino-7-oxononanoate aminotransferase apoenzyme (EC 2.6.1.62)

Query= BRENDA::Q88RB9
         (425 letters)



>IMG__ChlphaBS1_FD:642684930
          Length = 434

 Score =  160 bits (405), Expect = 7e-44
 Identities = 118/351 (33%), Positives = 177/351 (50%), Gaps = 19/351 (5%)

Query: 25  PIFVDTAKNSTVIDVE-GRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLA 83
           P++     +   I++E GR LID          G+ HP +  AV++QL K+SH  F    
Sbjct: 27  PVYPVKGASGVRIELEDGRRLIDGMSSWWAAIHGYNHPVLNEAVRKQLEKMSHVMFGGFT 86

Query: 84  YEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIARAATGRAG------VIAFTG 137
           +EP V L EK+  L PG   +K     +GS +VE A+K+A      AG      ++    
Sbjct: 87  HEPAVRLAEKLVDLTPGPL-QKVFFSDSGSVSVEVAIKMALQYHHAAGRPKKNRLLTIRS 145

Query: 138 GYHGRTMMTLGLTGKVVP-YSAGMGLMPGGIFRALFPSELHGISVDDAIASVERIFKNDA 196
           GYHG T   + +   V   +    G++P  +F        H +  DD+I    R  + + 
Sbjct: 146 GYHGDTFAAMSVCDPVTGMHGLFSGVLPQQLFAEAPACGFHDVWSDDSIGDFRR--QVEM 203

Query: 197 EPRDIAAIILEPV-QGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAM 255
             R+IAA+ILEPV QG GG      E + R+R LCD++ +LLI DE+ TG GRTG  FA+
Sbjct: 204 YHREIAAVILEPVVQGAGGMRFYSPEYLVRVRELCDRYDLLLIFDEIATGFGRTGKMFAL 263

Query: 256 EQMGVAPDLTTFAKSIAGGF-PLAGVCGKAEYMDAIA---PGGL--GGTYAGSPIACAAA 309
           E   V PD+    K++ GG+  LA      +    I+   PG    G T+  +P+ACA A
Sbjct: 264 EHADVVPDILCIGKALTGGYMTLAATLTNGDVSGVISNAEPGVFMHGPTFMANPLACAVA 323

Query: 310 LAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVEV 360
            A I++  E    +  + +  +L +GL E  +  P + DVR LG++  VE+
Sbjct: 324 SASIDLLAESDWRNSVRVIEAQLASGL-EPCRIVPGVADVRVLGAIGVVEL 373


Lambda     K      H
   0.320    0.138    0.395 

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: 471
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: 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