Alignments for a candidate for glpV in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpV in Azospirillum brasilense Sp245

Align GlpV, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate AZOBR_RS25900 AZOBR_RS25900 ABC transporter substrate-binding protein

Query= TCDB::G3LHZ3
         (569 letters)



>FitnessBrowser__azobra:AZOBR_RS25900
          Length = 584

 Score =  872 bits (2252), Expect = 0.0
 Identities = 418/567 (73%), Positives = 477/567 (84%), Gaps = 4/567 (0%)

Query: 2   TTTAGLLLAMTASAYAGMDEAKTFLDKEVGDLSTLPRADQEKEMQWFVDAAKPFAGMDIK 61
           + +A  LL  +A A+A ++ AK ++D E    STL + DQ KEMQWF+DAAKPFAGM+I 
Sbjct: 8   SASAAALLLSSAPAFADIEAAKRWIDSEFQP-STLSKEDQLKEMQWFIDAAKPFAGMEIN 66

Query: 62  VVSETITTHEYESKVLAPAFTAITGIKITHDLIGEGDVVEKLQTQMQSGENIYDAYINDS 121
           VVSETITTHEYE++ LA AF+ ITGIK+ HDLI EGDVVEK+QTQMQSG+NIYDA+INDS
Sbjct: 67  VVSETITTHEYEARTLARAFSEITGIKLRHDLIQEGDVVEKIQTQMQSGKNIYDAWINDS 126

Query: 122 DLIGTHWRYQQARSLTDWMANEGKDVTNPGLDIDDFIGKSFTTAPDGKLYQLPDQQFANL 181
           DLIGTH+RY+Q   LTDWM  EGKDVT P LD+ DFIG SFTTAPDGKLYQLPDQQFANL
Sbjct: 127 DLIGTHFRYKQVVPLTDWMDGEGKDVTLPTLDVKDFIGTSFTTAPDGKLYQLPDQQFANL 186

Query: 182 YWFRYDWFNDEKNKADFKAKYGYDLGVPVNWSAYEDIAEFFTG--REIDGKKVFGHMDYG 239
           YWFRYDWF +   KA FKAKYGYDLGVPVNWSAYEDIAEFFT   +EIDG KV+GHMDYG
Sbjct: 187 YWFRYDWFTNPDIKAKFKAKYGYDLGVPVNWSAYEDIAEFFTNDVKEIDGVKVYGHMDYG 246

Query: 240 KKDPSLGWRFTDAWLSMAGNGDKGIPNGKPVDEWGIKVDENSRPVGSCVARGGDTNGPAA 299
           KKDPSLGWRFTDAWLSMAGNGDKG+PNGKPVDEWGI++ E   PVGS + RGGDTNGPAA
Sbjct: 247 KKDPSLGWRFTDAWLSMAGNGDKGLPNGKPVDEWGIRM-EGCSPVGSSIERGGDTNGPAA 305

Query: 300 VYSIQKYLDWMKAYAPAAAQGMTFSESGPVPSQGEVAQQMFTYTAFTADFVKEGLPVVNA 359
           VYS+ KY++W+K YAP  A GMTFSESGPVP+QG VAQQMF YTAFTAD VK+GLPVVNA
Sbjct: 306 VYSVTKYVEWLKKYAPPQAAGMTFSESGPVPAQGNVAQQMFWYTAFTADMVKDGLPVVNA 365

Query: 360 DGTPKWRFAPSPHGVYWKDGMKLGYQDAGSWTLMKSTPDDRAKAAWLYAQFVTSKTVDVK 419
           DGTPKWR APSP G YWKDGMKLGYQDAGSWTL+KSTP DR KAAWLYAQF  SK+V +K
Sbjct: 366 DGTPKWRMAPSPKGAYWKDGMKLGYQDAGSWTLLKSTPVDRRKAAWLYAQFTMSKSVSLK 425

Query: 420 KSHMGLTFIRQSTLDHKSFTDRAPKLGGLIEFYRSPARLQWSPTGTNVPDYPKLAQLWWQ 479
           KSH+GLTFIR+S +  KSFT+RAPKLGGL+EFYRSPAR+QW+PTG NVPDYPKLAQLWWQ
Sbjct: 426 KSHVGLTFIRESDIWDKSFTERAPKLGGLVEFYRSPARVQWTPTGVNVPDYPKLAQLWWQ 485

Query: 480 AIGDASSGAKTAQEAMDSLCSEQEKVLQRLERAKVQGDIGPKLAEEHDLAYWNADAVKNG 539
            IGDASSGAKT Q AMD+L + Q+ V++RLER+ VQG+ GPKL ++    +W A A K+G
Sbjct: 486 NIGDASSGAKTPQAAMDALAAAQDSVMERLERSGVQGECGPKLNKKESAEFWFAKAEKDG 545

Query: 540 NLAPQLKIENEKDKPVTVNYDELVKSW 566
             APQ K+ NEK K  TV+YD+L+KSW
Sbjct: 546 TTAPQRKLSNEKPKGETVDYDQLIKSW 572


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: 1349
Number of extensions: 53
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: 584
Length adjustment: 36
Effective length of query: 533
Effective length of database: 548
Effective search space:   292084
Effective search space used:   292084
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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