Alignments for a candidate for mtlE in Xenophilus azovorans DSM 13620

GapMind for catabolism of small carbon sources

Alignments for a candidate for mtlE in Xenophilus azovorans DSM 13620

Align ABC transporter for D-Sorbitol, periplasmic substrate-binding component (characterized)
to candidate WP_038211953.1 Q392_RS21220 sugar ABC transporter substrate-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_2944
         (443 letters)



>NCBI__GCF_000745855.1:WP_038211953.1
          Length = 436

 Score =  699 bits (1803), Expect = 0.0
 Identities = 336/434 (77%), Positives = 377/434 (86%)

Query: 10  RLALAAAALAASLCGAAAHAQTELVIATVNNGHMIEMQKLSKNFEQAHPDIKLKWVTLEE 69
           R A +   LA +  G AA A TELVIATVNNGHMIEMQKL+ +FE+A+PDIKLKWVTLEE
Sbjct: 3   RFARSGLVLALATAGLAAQAATELVIATVNNGHMIEMQKLTPHFEKANPDIKLKWVTLEE 62

Query: 70  GVLRQRVTTDIATKGGQFDVMTIGMYEAPIWGKKGWLQELKTDAAYDVDDLLPAVRNGLS 129
           GVLRQRVTTDIATKGGQFDVMTIG+YEAPIW KKGWL+ + TDAAYDVDDLLPA+R+GLS
Sbjct: 63  GVLRQRVTTDIATKGGQFDVMTIGLYEAPIWSKKGWLKPIATDAAYDVDDLLPAIRSGLS 122

Query: 130 IDGKLFAAPFYGESSMLMYRKDLADKAGVQVPERPTWPQIKDLAAKIHDPKNGVYGICLR 189
            +GKL+AAPFYGESSMLMYRKDLADKAGV +PE+PTW Q+K+ A K +DPK GVYG+CLR
Sbjct: 123 HEGKLYAAPFYGESSMLMYRKDLADKAGVTLPEQPTWQQVKEFADKANDPKAGVYGMCLR 182

Query: 190 GKPGWGDNMAFLSTLVNTFGGQWFDMQWKPQLESKPWKEAITFYVDLLKNYGPPGSSANS 249
           GKPGWGDNMA L+TL NT+GGQWFD  WKPQL++  WKEAI+FYVDL+K  GPPG+SANS
Sbjct: 183 GKPGWGDNMALLTTLANTWGGQWFDTAWKPQLDTPAWKEAISFYVDLMKKDGPPGASANS 242

Query: 250 FNEILALTNSGKCGMWIDATIAASFVSDPKQSKVADQMAFAQAPTMNTPKGANWLWSWNL 309
           FNE LAL N GKC  W+DATIAASF+SDPKQSKVAD++AFAQAP   TPKGANWLWSWNL
Sbjct: 243 FNENLALFNEGKCAAWVDATIAASFISDPKQSKVADKVAFAQAPIAKTPKGANWLWSWNL 302

Query: 310 AIPAGSKKVDAAQKFITWSTSKEYVQLVAKTNGWANVPTGTRKSTYASPEFQKAARFAAA 369
           AIPA S K +AAQKFI W+TSK+Y+QLVAK +GW  VPTGTRKSTYA+PEFQK A+FA A
Sbjct: 303 AIPASSTKDEAAQKFIRWATSKDYIQLVAKEHGWHAVPTGTRKSTYANPEFQKVAKFAEA 362

Query: 370 EKVAIDSANPTDSTLPKSPYVGVQFAAIPEFQAIGIAVGQQMSAALAGKTTVDAALKASQ 429
           EK AIDSANP DSTLPKSPY GVQ+AAIPEFQAIG+ VGQQMSAALAGK TV+ ALK SQ
Sbjct: 363 EKKAIDSANPNDSTLPKSPYQGVQYAAIPEFQAIGVGVGQQMSAALAGKVTVEQALKTSQ 422

Query: 430 VSADREMKKAGYYK 443
             A+REMKK GYYK
Sbjct: 423 TLAEREMKKGGYYK 436


Lambda     K      H
   0.316    0.129    0.394 

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: 731
Number of extensions: 21
Number of successful extensions: 1
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: 443
Length of database: 436
Length adjustment: 32
Effective length of query: 411
Effective length of database: 404
Effective search space:   166044
Effective search space used:   166044
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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)
SQLite3 databases

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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 2024 update 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