Alignments for a candidate for xacD in Herbaspirillum autotrophicum IAM 14942

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacD in Herbaspirillum autotrophicum IAM 14942

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_050463099.1 AKL27_RS12200 dihydroxy-acid dehydratase

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



>NCBI__GCF_001189915.1:WP_050463099.1
          Length = 575

 Score =  872 bits (2254), Expect = 0.0
 Identities = 427/576 (74%), Positives = 494/576 (85%), Gaps = 4/576 (0%)

Query: 4   SNQTKKPLRSQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHF 63
           S+  K   RSQAWFG +DRDGF++RSW+KN+GIPHD+FDGRPVIGICNT+SELTPCN+HF
Sbjct: 2   SDTKKITRRSQAWFGRQDRDGFIYRSWVKNRGIPHDQFDGRPVIGICNTYSELTPCNSHF 61

Query: 64  RELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVIL 123
           R LAE VK GV EAGG PLEFPVMSLGET LRPTAMLFRNLASMDVEESIR NP+DGV+L
Sbjct: 62  RALAEQVKIGVWEAGGFPLEFPVMSLGETLLRPTAMLFRNLASMDVEESIRANPLDGVVL 121

Query: 124 LVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQ 183
           L+GCDKTTPALLMGAAS ++P + VSGGPMLNG++RG  +GSGTGVWQMSEEVR G MTQ
Sbjct: 122 LMGCDKTTPALLMGAASVDVPTIGVSGGPMLNGKYRGGELGSGTGVWQMSEEVRGGKMTQ 181

Query: 184 EEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRR 243
           EEF EAESCM+RS GHCMTMGTASTMASMVE+LGM LP NAAIPAVDARR VLA  +GRR
Sbjct: 182 EEFFEAESCMHRSHGHCMTMGTASTMASMVEALGMSLPGNAAIPAVDARRNVLARNSGRR 241

Query: 244 IVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDW-ELG 302
           IV+MV+ED  M KILTR AFENAIR NAAIGGSTNAV+HL+A+A RIGV L+L DW ++G
Sbjct: 242 IVEMVQEDFVMSKILTRAAFENAIRVNAAIGGSTNAVIHLLAIAGRIGVNLNLADWDDIG 301

Query: 303 SNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAAN 362
            ++PCL+NLQPSG+YLMEDFYYAGGLPAV+++L  + ++ K AL+ NG+TLWDN + A N
Sbjct: 302 QHLPCLLNLQPSGKYLMEDFYYAGGLPAVIREL--ESVIDKGALSANGQTLWDNCKEAPN 359

Query: 363 YDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHA 422
           ++  VI  F  PFKP AGIAVL GNL P+GAVIKPSAAT +LLKH GRAVVFEN ++LH 
Sbjct: 360 WNRDVIHAFDAPFKPAAGIAVLHGNLCPDGAVIKPSAATPALLKHTGRAVVFENSDDLHK 419

Query: 423 KIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSGTA 482
           +IDDE LD+DE C++VLK  GPKGYPG  E GNMPLP KVL+KG+TDMVR+SD RMSGTA
Sbjct: 420 RIDDEDLDVDETCVLVLKNCGPKGYPGMGEAGNMPLPPKVLRKGVTDMVRVSDARMSGTA 479

Query: 483 YGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAPEAP-K 541
           YG VVLHV+PEAAAGGPLA VQ GDM+ELDVE R+LHL V+DEEL RRRA W+APE P K
Sbjct: 480 YGTVVLHVTPEAAAGGPLALVQNGDMVELDVEARKLHLHVSDEELERRRANWKAPEPPMK 539

Query: 542 RGYYKLYVEHVLQADQGADLDFLVGSSGAPVPRDSH 577
           RG+ KLY++HV QA+ GADLDFLVG SGA +P+D+H
Sbjct: 540 RGWTKLYIDHVQQANLGADLDFLVGKSGAGIPKDNH 575


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: 1141
Number of extensions: 44
Number of successful extensions: 6
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: 575
Length adjustment: 36
Effective length of query: 541
Effective length of database: 539
Effective search space:   291599
Effective search space used:   291599
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 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
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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
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