GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Lutibaculum baratangense AMV1

Align 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_023433142.1 N177_RS14610 enoyl-CoA hydratase

Query= reanno::BFirm:BPHYT_RS13545
         (706 letters)



>NCBI__GCF_000496075.1:WP_023433142.1
          Length = 688

 Score =  458 bits (1179), Expect = e-133
 Identities = 269/678 (39%), Positives = 381/678 (56%), Gaps = 15/678 (2%)

Query: 26  APVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREFGKPPVPPSLPDV 85
           APV    ADVR  L+  + AA     V A+++     + + GAD  E  +    P+L D+
Sbjct: 25  APV--FGADVRAALIGGLRAALLRPDVRAIVLAIPEGSAMMGADEGEIEEACKAPTLMDL 82

Query: 86  CNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQLGLLPGAGGTQRT 145
              +E   KPVVAA+ G+ LG G E ALA H R+A   A+LGLP  + G++P  G  QR 
Sbjct: 83  QAEVEDAAKPVVAALSGSVLGAGFEFALACHGRVASKTARLGLPHAKFGMMPLGGAIQRL 142

Query: 146 PRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYVHELLAAHAPVRRT 205
            RL G +  LD++LSG    A  A   G++D +   DD+ A   A+ H +       RR 
Sbjct: 143 SRLAGIRVTLDMVLSGTAIDAAAAEEAGIVDWV-VEDDLTAAASAFAHCIAEGEQASRRA 201

Query: 206 RDAAALSDRAASLAAVATARAETAKKSRGLFSPLKIVDAVEAAIEQPFDEGLRVERKLFL 265
            D   + DR      ++ A     +K RG       + A+  A E PFDEGL  E +L L
Sbjct: 202 GDLD-VPDRDEKQDILSGAIRTHGRKLRGTRQLELTLSALRVAAETPFDEGLATETELSL 260

Query: 266 ECIDSPQRAGLIHAFFAEREVLKAPETRA-AKPRTLNTIGVVGGGTMGAGIAVAVLDAGL 324
           E     + +   H   AERE  + P+  A  +   +  +G+VG GTMG GIA+  L+ GL
Sbjct: 261 ELARGAEASARRHVARAERETWRIPDIPAETETLPVERVGIVGAGTMGGGIAMNFLNTGL 320

Query: 325 PVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAALMSRWSGSTSYDALAGADLVI 384
           PVT++E    +L RG + I + YDG   KGR+S +     M   +G+ + + LA  DLVI
Sbjct: 321 PVTIVETRQEALDRGVSVIRRNYDGSARKGRMSQDDVEVRMRLLTGTLALEDLASCDLVI 380

Query: 385 EAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYLDIDALASSVSRPADVIGLHFFSPANI 444
           EAVFE++ VK+ +F  LD + +  A+LA+NTSYLD+D +A + SRP  V+GLHFFSPANI
Sbjct: 381 EAVFENMEVKKEIFGRLDAIVRPDAILASNTSYLDVDEIARATSRPERVLGLHFFSPANI 440

Query: 445 MKLLEVVVPKQVSADVVATAFELAKKLRKTPVRAGVCDGFIGNRVLAVYRSAADAMMEDG 504
           M+LLEVV  ++ S  V+AT  +LA+++ K  V  GVC GF+GNR+LA  +  A  ++ +G
Sbjct: 441 MRLLEVVRAEKTSKPVLATTMQLARRIGKVGVMVGVCFGFVGNRMLAQRQREATKLILEG 500

Query: 505 ASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAARKRRAATRNPAARYVQIADRLCERGW 564
           A P+ +D  +  FG PMGPF + DLAG D+GW+    +  T         + + LCE   
Sbjct: 501 AMPWDVDRVLYDFGLPMGPFAMSDLAGLDLGWSRETSKGET---------VKEILCEMDR 551

Query: 565 FGQKSGRGFYLYPEGSRSGTPDPEVEAIIDAERARAGITPRSFTDEEIIRRYMAAMINEG 624
            GQK+G GFY Y E +R   P    E +I     R G+  R   DEEI++R +  MINEG
Sbjct: 552 RGQKTGAGFYDYDE-NRKAVPSKVTETVILDLAERRGMARREIADEEILKRCIYPMINEG 610

Query: 625 ANVVHERIALRPLDVDVTFLYGYGFPRYRGGPMKYADMVGLPKILADIREFAKEDPLFWK 684
           A ++ E  A+R  D+DV ++ GYG+P +RGGPM Y D +GL ++L  +R F       ++
Sbjct: 611 AKILDEGKAIRASDIDVVWINGYGWPAHRGGPMYYGDRIGLDEVLETMRRFEATQGEDFR 670

Query: 685 PSPLLIELVERGADFASL 702
           P+PLL  LV  G  F  L
Sbjct: 671 PAPLLERLVREGRGFGDL 688


Lambda     K      H
   0.320    0.136    0.392 

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: 1031
Number of extensions: 50
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 706
Length of database: 688
Length adjustment: 39
Effective length of query: 667
Effective length of database: 649
Effective search space:   432883
Effective search space used:   432883
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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