GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuA in Pseudomonas fluorescens FW300-N2C3

Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate AO356_15445 AO356_15445 acyl-CoA dehydrogenase

Query= SwissProt::P33224
         (541 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_15445 AO356_15445 acyl-CoA
           dehydrogenase
          Length = 549

 Score =  394 bits (1013), Expect = e-114
 Identities = 217/462 (46%), Positives = 285/462 (61%), Gaps = 7/462 (1%)

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

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

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

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

Query: 240 VPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKMGGMTR 299
           +PR  PD  RN   ++RLK+KLGN SNAS EVEF+ A+ W++G EG G+  I++M  MTR
Sbjct: 245 LPRHRPDDTRNQFYIQRLKNKLGNCSNASSEVEFRGALAWMVGEEGRGVPTIIEMVAMTR 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 E+S LPRLYRE P
Sbjct: 365 RALDHLNDEHEAKFARLVTAVGKYWICKRAPAMINEAAECMGGAGYVEDSILPRLYREAP 424

Query: 420 VNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDR 461
           VNS WEGSGN+ CLDVLR L+K+ GV ++L     +  G  R
Sbjct: 425 VNSTWEGSGNVQCLDVLRALSKEPGVLEVLFSELGDGHGDKR 466


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: 685
Number of extensions: 26
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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