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.

Links

Downloads

Related tools

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