GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Algiphilus aromaticivorans DG1253

Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate WP_156966386.1 U743_RS08760 DNA alkylation response protein

Query= SwissProt::P33224
         (541 letters)



>NCBI__GCF_000733765.1:WP_156966386.1
          Length = 560

 Score =  404 bits (1037), Expect = e-117
 Identities = 219/513 (42%), Positives = 305/513 (59%), Gaps = 9/513 (1%)

Query: 5   THTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLANV 64
           TH V NQP PL + N +  D AL EAV REG  W  + L + G + G+ E +  G  AN 
Sbjct: 16  THEVTNQPPPLQDYNAFEGDTALVEAVKREGGAWGIEALRADGARTGSEEVISWGYRANA 75

Query: 65  NPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFMLH 124
             PEL  +D QG R+D V +H  +H LM       +H+  W  D + GA V R+A   +H
Sbjct: 76  YKPELQAFDRQGHRIDQVAYHEDYHRLMAHSLQAGIHSSPWA-DPKPGAHVVRSALQYMH 134

Query: 125 AQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMGM 184
            QV+AG  CP+TMTFA  P + +  P+  + W   +L+  YD   +P  QKR L +GMGM
Sbjct: 135 YQVDAGHHCPVTMTFACVPAI-RTTPSVAEQWLPGILTADYDPRDIPHTQKRALTVGMGM 193

Query: 185 TEKQGGSDVMSNTTRAERLEDGS-----YRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFF 239
           TEKQGGSDV  NTT A  + +G+     Y L+GHKWF S P  DA L+LAQT GGLSCF 
Sbjct: 194 TEKQGGSDVRINTTSARPVGNGTGPGAVYELLGHKWFTSAPMCDAFLMLAQTEGGLSCFL 253

Query: 240 VPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTR 299
           VPR+  DG +N I+++RLK+K GN SNAS E+E + A G +LG EG G+  I++M  MTR
Sbjct: 254 VPRWREDGSKNPIQVQRLKNKAGNVSNASSEIELRGAQGRMLGEEGRGVPTIIEMVAMTR 313

Query: 300 FDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLA 359
           +DC +GS A MR+A + AI+H   R  FG  LI+QP M +VL+ + L++EG  AL  R+ 
Sbjct: 314 YDCMVGSTASMRQATAQAIHHCAHREAFGKRLIEQPAMANVLADLQLEVEGALALTMRMG 373

Query: 360 RAWDRRADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMP 419
           RA D   D  E L  RL  P  K+ ICKR      EAME +GG G  ++  + RLYR+ P
Sbjct: 374 RALDNPDDEHEKLLLRLGLPTGKYWICKRNPNHTYEAMECIGGNGVMDDFIMARLYRDAP 433

Query: 420 VNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQL--RKP 477
           +N+IWEGSGN+  LD+LR ++K     ++        +G   +FD A+  L   L  ++ 
Sbjct: 434 INAIWEGSGNVQALDLLRAMSKSPAALEVFLGELEAARGMHDHFDAALDHLHAALSDQEA 493

Query: 478 AEELGREITHQLFLLGCGAQMLKYASPPMAQAW 510
            E   R++  ++ L    + +L++ +  +A+A+
Sbjct: 494 LEHRARDLAERMALCMQASLLLRHGNARVAEAF 526


Lambda     K      H
   0.324    0.138    0.428 

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: 703
Number of extensions: 29
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: 541
Length of database: 560
Length adjustment: 36
Effective length of query: 505
Effective length of database: 524
Effective search space:   264620
Effective search space used:   264620
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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