GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Pseudomonas fluorescens FW300-N1B4

Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate Pf1N1B4_2720 Acyl-CoA dehydrogenase (EC 1.3.8.7)

Query= SwissProt::P33224
         (541 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2720
          Length = 549

 Score =  400 bits (1029), Expect = e-116
 Identities = 229/502 (45%), Positives = 303/502 (60%), Gaps = 11/502 (2%)

Query: 4   QTHTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLAN 63
           +TH V NQP  L+ +NLY  D  L E   R  AGW    + + G   G    +E G  AN
Sbjct: 8   ETHEVTNQPPSLDGANLYRIDLPLQEWSRRFDAGWAESRIDAYGVLAG-GPLMEAGFAAN 66

Query: 64  VNPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFML 123
            N P  + +D  G R+D V FHPA+H LM+    + +  L W  D + GA VARA+   L
Sbjct: 67  QNKPVFVSHDRYGHRIDLVEFHPAYHELMRTAVEHGLTGLPWT-DPQPGAHVARASMTYL 125

Query: 124 HAQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMG 183
           H+Q EAGS CP+TMTFA+ P + ++ P   + W   +L+  YD   +    K G+ IGM 
Sbjct: 126 HSQAEAGSGCPLTMTFASVPAM-RLQPDLAKQWLPKILATEYDPRNVGMAHKAGVTIGMA 184

Query: 184 MTEKQGGSDVMSNTTRAERLEDG----SYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFF 239
           MTEKQGG+DV +NTT+A  +       +Y LVGHKWF S P  DA L LAQT  GL+CF 
Sbjct: 185 MTEKQGGTDVRANTTKAYPVGASGPGQAYELVGHKWFCSAPMCDAFLTLAQTDKGLTCFL 244

Query: 240 VPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTR 299
           +PR  PD  RN   ++RLK+KLGN SNAS EVEF+ A+ W++G EG G+  I++M  MTR
Sbjct: 245 LPRHRPDDSRNQFYIQRLKNKLGNWSNASSEVEFRGALAWMVGEEGRGVPTIIEMVAMTR 304

Query: 300 FDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTALLFRLA 359
           FDC +GS A+MR+A + A +H   R V G  L +QPLM++VL+ +AL+ E   AL  R+ 
Sbjct: 305 FDCMVGSSALMRQALTQASHHCAHRKVGGKLLSEQPLMQNVLADLALESEAALALSLRMG 364

Query: 360 RAWDRRADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPRLYREMP 419
           RA D   D  EA +ARL T   K+ ICKR    + EA E +GG GY EES LPRLYRE P
Sbjct: 365 RALDHLDDDHEAKFARLVTAVGKYWICKRAPAMINEAAECMGGAGYVEESILPRLYREAP 424

Query: 420 VNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQLRKPA- 478
           VNS WEGSGN+ CLDVLR L+K+ GV D+L     +  G D+     + +LQ   +  A 
Sbjct: 425 VNSTWEGSGNVQCLDVLRALSKEPGVLDVLFSELGDGHG-DKRLAAHISQLQAAFKDTAD 483

Query: 479 -EELGREITHQLFLLGCGAQML 499
            +   R++T  +  LG  A++L
Sbjct: 484 IQYRARQLTEDI-ALGLQAKLL 504


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: 670
Number of extensions: 22
Number of successful extensions: 5
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: 549
Length adjustment: 35
Effective length of query: 506
Effective length of database: 514
Effective search space:   260084
Effective search space used:   260084
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: 52 (24.6 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