GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Pseudomonas simiae WCS417

Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate GFF4807 PS417_24590 acyl-CoA dehydrogenase

Query= SwissProt::P33224
         (541 letters)



>FitnessBrowser__WCS417:GFF4807
          Length = 550

 Score =  408 bits (1049), Expect = e-118
 Identities = 230/476 (48%), Positives = 297/476 (62%), Gaps = 12/476 (2%)

Query: 4   QTHTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLAN 63
           +TH V NQP  L+ +NLY  D  L E   R GAGW    + + G   G    +E G LAN
Sbjct: 8   ETHDVTNQPPSLDGTNLYRIDVPLQEWSRRFGAGWAQARIDAYGALAG-GPLMEAGFLAN 66

Query: 64  VNPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFML 123
            N P    +D  G R+D V FHPA+H LM+    + + +L W    +SGA VARAA   L
Sbjct: 67  QNKPVFSSHDRYGHRIDLVEFHPAYHELMRTAVEHGLPSLPWAHP-QSGAHVARAAMTYL 125

Query: 124 HAQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGMG 183
           H+Q EAG+ CP+TMTFA  P L ++ P   + W   +L+ +YD   +    K G  +GM 
Sbjct: 126 HSQAEAGTGCPLTMTFACVPAL-RLQPDLAETWLPKILTTQYDPRNVGIAHKAGATLGMA 184

Query: 184 MTEKQGGSDVMSNTTRAERLEDG----SYRLVGHKWFFSVPQSDAHLVLAQTAGGLSCFF 239
           MTEKQGG+DV +NTTRA  +  G    +Y LVGHKWF S P  DA L LAQT  GLSCF 
Sbjct: 185 MTEKQGGTDVRANTTRAYPVGAGGPGQAYELVGHKWFCSAPMCDAFLTLAQTDKGLSCFL 244

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

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

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

Query: 420 VNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQLR 475
           VNS WEGSGN+ CLDVLR L+K+ GV + L   FVE+   D + DR + R  +QL+
Sbjct: 425 VNSTWEGSGNVQCLDVLRALSKEPGVLEAL---FVEL--GDGHGDRLLARHIEQLK 475


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: 24
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: 550
Length adjustment: 35
Effective length of query: 506
Effective length of database: 515
Effective search space:   260590
Effective search space used:   260590
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