Alignments for a candidate for fadB in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Pseudomonas putida KT2440

Align 3-hydroxyadipyl-CoA dehydrogenase; EC 1.1.1.- (characterized)
to candidate PP_3282 PP_3282 3-hydroxyadipyl-CoA dehydrogenase

Query= SwissProt::P76083
         (475 letters)



>FitnessBrowser__Putida:PP_3282
          Length = 505

 Score =  397 bits (1019), Expect = e-115
 Identities = 234/490 (47%), Positives = 300/490 (61%), Gaps = 29/490 (5%)

Query: 4   NVQTVAVIGSGTMGAGIAEVAASHGHQVLLYDISAEALTRAIDGIHARLNSRVTRGKLTA 63
           NVQ VAVIG+G MGAGIA+VAA  GH V LYD    A  +A+ GI  +L   V +GKL A
Sbjct: 7   NVQ-VAVIGAGAMGAGIAQVAAQAGHPVKLYDNRPGAAAQAVTGIDRQLARLVDKGKLLA 65

Query: 64  ETCERTLKRLIPVTDIHALAAADLVIEAASERLEVKKALFAQLAEVCPPQTLLTTNTSSI 123
              E    RL PV  + ALA A LVIEA  E L+VK+ALF+QL  +C    +L +NTSS+
Sbjct: 66  AERETINARLCPVDTLEALADAGLVIEAIVENLQVKQALFSQLETLCAADCILASNTSSL 125

Query: 124 SITAIAAEIKNPERVAGLHFFNPAPVMKLVEVVSGLATAAEVVEQLCELTLSWGKQPVRC 183
           SIT++AA ++ P+ V G+HFFNPAP+M LVEVVSGLAT   V   +     +WGKQPV  
Sbjct: 126 SITSLAAGLERPQHVVGMHFFNPAPLMALVEVVSGLATDPAVAACIYATAQAWGKQPVHA 185

Query: 184 HSTPGFIVNRVARPYYSEAWRALEEQVAAPEVIDAALRDGAGFPMGPLELTDLIGQDVNF 243
            STPGFIVNRVARP+Y+E+ R L+E  A    +DA +RD  GF MG  ELTDLIG DVN+
Sbjct: 186 RSTPGFIVNRVARPFYAESLRLLQEGAADCASLDALMRDSGGFRMGAFELTDLIGHDVNY 245

Query: 244 AVTCSVFNAFWQERRFLPSLVQQELVIGGRLGKKSGLGVYDWR--------AEREAVVGL 295
           AVTCSVF+AF+ + RF PSLVQ+ELV  G LG+K+G G Y +         AE  +    
Sbjct: 246 AVTCSVFDAFYGDFRFQPSLVQKELVDAGHLGRKTGQGFYRYAEGVERPQPAELHSSACA 305

Query: 296 EA--VSDSFSPMK-------------VEKKSDGVTEIDDVLLIETQGETAQALA-----I 335
           EA  V  +   M+              ++   G+ ++ D  L  + G  A   A      
Sbjct: 306 EACVVEGNLGVMQPLVERLRQSGIAVTQRAGSGLIQVGDATLALSDGRLASQRAREDGLR 365

Query: 336 RLARPVVVIDKMAGKVVTIAAAAVNPDSATRKAIYYLQQQGKTVLQIADYPGMLIWRTVA 395
            L    + +D  +   + I+ +A   DSA  +A+  LQ+ G  V  +AD PG+++ RTVA
Sbjct: 366 NLVLLDLALDYSSATRIAISWSADTSDSARDQAVALLQRAGLKVTGVADLPGLVVLRTVA 425

Query: 396 MIINEALDALQKGVASEQDIDTAMRLGVNYPYGPLAWGAQLGWQRILRLLENLQHHYGEE 455
           M+ NEA DA+ +GV S  DID AMR GVNYP GPLAW A +G    LR+L+NLQ  YGE 
Sbjct: 426 MLANEAADAVLQGVGSAADIDLAMRAGVNYPCGPLAWAANIGIAHTLRVLDNLQCSYGES 485

Query: 456 RYRPCSLLRQ 465
           RYRP  LLR+
Sbjct: 486 RYRPSLLLRR 495


Lambda     K      H
   0.319    0.134    0.386 

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: 546
Number of extensions: 19
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: 475
Length of database: 505
Length adjustment: 34
Effective length of query: 441
Effective length of database: 471
Effective search space:   207711
Effective search space used:   207711
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 (21.8 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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources