GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Acidovorax sp. GW101-3H11

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate Ac3H11_3161 Citrate synthase (si) (EC 2.3.3.1)

Query= reanno::pseudo6_N2E2:Pf6N2E2_6062
         (375 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3161
          Length = 436

 Score =  183 bits (464), Expect = 9e-51
 Identities = 129/396 (32%), Positives = 200/396 (50%), Gaps = 40/396 (10%)

Query: 11  GLRGQVAGQTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYT 70
           G     A Q+A++ +      L YRGY +  LA +  F E  +LLLYG+LP  AQ   +T
Sbjct: 50  GFLSTAATQSAITYIDGDKGELLYRGYPIEQLAENCDFLETCHLLLYGDLPNAAQKIDFT 109

Query: 71  GKLRQLRDLPQALKEVLERIPADAHPMDVMRTGCSFLGNLEPEQDFSQQHDKTD------ 124
            ++     + + ++  L     DAHPM V+ TG   +G L      +  HD TD      
Sbjct: 110 SRVTNHTMVNEQMQFFLRGFRRDAHPMAVL-TG--LVGALS-----AFYHDSTDINNPEH 161

Query: 125 ------RLLAAFPAIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGKKPSELHV---- 174
                 RL+A  P ++   Y++   GQ      + +S  G+FL ++ G    E  V    
Sbjct: 162 RDISAIRLIAKMPTLVAMSYKYG-MGQPYMYPQNNLSYSGNFLRMMFGTPCEEYKVNPVL 220

Query: 175 -KVMNVSLILYAEHEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMI 233
            + ++   IL+A+HE NAST T R+C S+ ++ F+ I A +  L GP HGGANEAA+ M+
Sbjct: 221 ERALDRIFILHADHEQNASTSTVRLCGSSGTNPFAAIAAGVACLWGPAHGGANEAALNML 280

Query: 234 ERFSSP--QEAIEGTLGMLARKD---KIMGFGHAIYKDNDPRNEVIKGWSKKLADEVG-- 286
               +    E I   +  +  K+   K+MGFGH +YK+ DPR ++++    ++  E+G  
Sbjct: 281 YDIQAQGGVEKIGDFIKQVKDKNSGVKLMGFGHRVYKNYDPRAKLMQETCNEVLAELGLE 340

Query: 287 DTVLFPVSEAIDKTMWE-----QKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGW 341
           +  LF +++ ++K   E     Q+KL+PN DFY       +GIP  LFT IF  +R  GW
Sbjct: 341 NDPLFKLAKELEKIALEDDYFVQRKLYPNVDFYSGIVQRAIGIPVNLFTGIFSLARTVGW 400

Query: 342 AAHVFEQRAN--NRIIRPSAEYTGVEQRKFVPIEQR 375
            A + E   +   +I RP   +TG  +R   P+  R
Sbjct: 401 IAQLNEMIGDPEYKIGRPRQLFTGSVRRDVPPLASR 436


Lambda     K      H
   0.321    0.135    0.406 

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: 403
Number of extensions: 20
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: 375
Length of database: 436
Length adjustment: 31
Effective length of query: 344
Effective length of database: 405
Effective search space:   139320
Effective search space used:   139320
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: 50 (23.9 bits)

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:

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