Alignments for a candidate for glpV in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpV in Cereibacter sphaeroides ATCC 17029

Align GlpV, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_011840943.1 RSPH17029_RS06695 ABC transporter substrate-binding protein

Query= TCDB::G3LHZ3
         (569 letters)



>NCBI__GCF_000015985.1:WP_011840943.1
          Length = 574

 Score =  923 bits (2386), Expect = 0.0
 Identities = 441/571 (77%), Positives = 496/571 (86%), Gaps = 9/571 (1%)

Query: 2   TTTAGLLLAMTASAYAGMDEAKTFLDKEVGDLSTLPRADQEKEMQWFVDAAKPFAGMDIK 61
           T  A  L+A+ A A+A M+ AK FLD E+GDLS+L RA+QE EMQWF+DAA+PFAGM+IK
Sbjct: 8   TAMALCLMAVAAPAWADMEAAKKFLDAEIGDLSSLSRAEQEAEMQWFIDAAQPFAGMEIK 67

Query: 62  VVSETITTHEYESKVLAPAFTAITGIKITHDLIGEGDVVEKLQTQMQSGENIYDAYINDS 121
           VVSETITTHEYESKVLAPAF+AITGIKI+HDLIGEGDVVEKLQTQMQSGENIYDAYINDS
Sbjct: 68  VVSETITTHEYESKVLAPAFSAITGIKISHDLIGEGDVVEKLQTQMQSGENIYDAYINDS 127

Query: 122 DLIGTHWRYQQARSLTDWMANEGKDVTNPGLDIDDFIGKSFTTAPDGKLYQLPDQQFANL 181
           DLIGTHWRY+QARSLTDWMAN GKDVTNPGLD+ D+IG  FTTAPDG+LYQLPDQQFANL
Sbjct: 128 DLIGTHWRYKQARSLTDWMANAGKDVTNPGLDLQDYIGLKFTTAPDGELYQLPDQQFANL 187

Query: 182 YWFRYDWFNDEKNKADFKAKYGYDLGVPVNWSAYEDIAEFFTGREIDG----KKVFGHMD 237
           YWFR DWF+D   KA FK KYGY+LGVP+NWSAYEDIAEFFTGR++      K  FG MD
Sbjct: 188 YWFRADWFDDADTKAAFKEKYGYELGVPLNWSAYEDIAEFFTGRDMSALGGPKSAFGSMD 247

Query: 238 YGKKDPSLGWRFTDAWLSMAGNGDKGIPNGKPVDEWGIKVDENSRPVGSCVARGGDTNGP 297
           YGKKDPSLGWR+TDAW+SMAG GDKG PNG PVDEWGI+VDENSRPVGSCVARGG TN  
Sbjct: 248 YGKKDPSLGWRYTDAWMSMAGMGDKGDPNGLPVDEWGIRVDENSRPVGSCVARGGATNDA 307

Query: 298 AAVYSIQKYLDWMKAYAPAAAQGMTFSESGPVPSQGEVAQQMFTYTAFTADFVKEGLPVV 357
           AAVY+I K ++W++ YAP  A GMTFSESGPVP+QGEVAQQ+F YTAFTAD VKEGLPV+
Sbjct: 308 AAVYAITKSIEWLQKYAPPQAAGMTFSESGPVPAQGEVAQQIFWYTAFTADMVKEGLPVM 367

Query: 358 NADGTPKWRFAPSPHGVYWKDGMKLGYQDAGSWTLMKSTPDDRAKAAWLYAQFVTSKTVD 417
           N DGTPKWR APSPHG YW +G K+GYQD GSWTL+KSTPD+RAKAAWLYAQFV+SKTVD
Sbjct: 368 NEDGTPKWRMAPSPHGAYWSEGTKVGYQDVGSWTLLKSTPDERAKAAWLYAQFVSSKTVD 427

Query: 418 VKKSHMGLTFIRQSTLDHKSFTDRAPKLGGLIEFYRSPARLQWSPTGTNVPDYPKLAQLW 477
           VKKSH+GLTF+R+ST+ H+SFTDRAPKLGGL+EFYRSPAR+QWSPTGTNVPDYPKLAQLW
Sbjct: 428 VKKSHVGLTFVRESTIQHQSFTDRAPKLGGLVEFYRSPARVQWSPTGTNVPDYPKLAQLW 487

Query: 478 WQAIGDASSGAKTAQEAMDSLCSEQEKVLQRLERAKVQGDIGPKLAEEHDLAYWNADAVK 537
           WQ IGDA SGAK+ QEA+D+LC+EQEKV+ RLERA VQGD+GPKL EE D   W  DA  
Sbjct: 488 WQNIGDAMSGAKSPQEALDALCAEQEKVMARLERAGVQGDLGPKLNEEKDPQEW-LDAPG 546

Query: 538 NGNLAPQLKIENEKDKPVTVNYDELVKSWQK 568
               AP  K+ENEK +  T++YDEL+KSWQK
Sbjct: 547 ----APVAKLENEKPQGETISYDELIKSWQK 573


Lambda     K      H
   0.315    0.132    0.409 

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: 1372
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: 569
Length of database: 574
Length adjustment: 36
Effective length of query: 533
Effective length of database: 538
Effective search space:   286754
Effective search space used:   286754
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 (21.5 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 10 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)
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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