Alignments for a candidate for xacD in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacD in Phaeobacter inhibens BS107

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate GFF723 PGA1_c07380 dihydroxy-acid dehydratase IlvD

Query= reanno::BFirm:BPHYT_RS19730
         (577 letters)



>FitnessBrowser__Phaeo:GFF723
          Length = 571

 Score =  733 bits (1891), Expect = 0.0
 Identities = 364/570 (63%), Positives = 445/570 (78%), Gaps = 2/570 (0%)

Query: 9   KPLRSQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHFRELAE 68
           K  R++AW+G  D+DGF+HRSWMKNQG P   FDGRP+IGICNTWSELTPCN+  R+LAE
Sbjct: 3   KDRRNRAWYGKLDKDGFIHRSWMKNQGFPDHAFDGRPIIGICNTWSELTPCNSGLRDLAE 62

Query: 69  YVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVGCD 128
            VK+GV EAGG P+EFPVMSLGET ++PTAMLFRNL +MDVEESIR   +DGV+LL GCD
Sbjct: 63  GVKRGVWEAGGFPVEFPVMSLGETQMKPTAMLFRNLLAMDVEESIRAYGIDGVVLLGGCD 122

Query: 129 KTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQEEFTE 188
           KTTP  LMGAAS +LPA+ VS GPMLNG+++GK+IGSGT VW+ SE VRAG MT ++F  
Sbjct: 123 KTTPGQLMGAASVDLPAIVVSSGPMLNGKWQGKDIGSGTDVWKFSEAVRAGEMTLQDFMA 182

Query: 189 AESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDMV 248
           AES M+RS+G CMTMGTASTMAS+VE++GM LP NAA+PAVDARR  LAHL G+RIV+MV
Sbjct: 183 AESGMSRSKGVCMTMGTASTMASLVEAMGMSLPTNAALPAVDARRMALAHLTGKRIVEMV 242

Query: 249 REDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWELGSNVPCL 308
            ED+    +LTR+AF NAI  NAA+GGSTNAVVHL+ALA R+G ELSL+D++LGS++P L
Sbjct: 243 EEDIKPSDVLTREAFVNAIMANAAVGGSTNAVVHLLALAGRVGAELSLDDFDLGSDIPLL 302

Query: 309 VNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANYDEKVI 368
           VN  PSG+YLMEDF YAGG+P VLKQL + G L     TV G  +      A  +++ VI
Sbjct: 303 VNCMPSGKYLMEDFCYAGGMPVVLKQLADNGHLRSNT-TVLGGDILAYAEGAECFNDDVI 361

Query: 369 TTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHAKIDDES 428
            +F EP KP AG+ VL+GNLAPNGA++KPSAAT  LL+H G A VFE IE++ A ID + 
Sbjct: 362 KSFDEPVKPAAGLRVLRGNLAPNGAIVKPSAATDHLLEHEGVAHVFETIEDMKANIDRDD 421

Query: 429 LDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSGTAYGAVVL 488
           L + +  I+VLKG GPKGYPG  EVGNMP+P+K++++G+ DM+RISDGRMSGTA+G V+L
Sbjct: 422 LPVTKDSILVLKGVGPKGYPGMPEVGNMPIPRKLVREGVRDMIRISDGRMSGTAFGTVIL 481

Query: 489 HVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQ-APEAPKRGYYKL 547
           HVSPE+ AGGPL  VQTGD I +  +   L L V++EEL  RR AWQ  P    RGY KL
Sbjct: 482 HVSPESQAGGPLGLVQTGDRIRVSAKNGTLDLLVSEEELTARREAWQPEPLHYTRGYAKL 541

Query: 548 YVEHVLQADQGADLDFLVGSSGAPVPRDSH 577
           YV+ VLQA++GADLDFLVG    PV R+SH
Sbjct: 542 YVDSVLQAEKGADLDFLVGKDTRPVTRESH 571


Lambda     K      H
   0.318    0.135    0.401 

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: 1042
Number of extensions: 47
Number of successful extensions: 3
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: 577
Length of database: 571
Length adjustment: 36
Effective length of query: 541
Effective length of database: 535
Effective search space:   289435
Effective search space used:   289435
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
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
the source code
instructions for running GapMind on your computer

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