Alignments for a candidate for glpV in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpV in Marinobacter adhaerens HP15

Align ABC transporter for Glycerol, periplasmic substrate-binding component (characterized)
to candidate GFF2216 HP15_2170 ABC-type sugar transport system, periplasmic component

Query= reanno::acidovorax_3H11:Ac3H11_796
         (577 letters)



>FitnessBrowser__Marino:GFF2216
          Length = 594

 Score =  686 bits (1770), Expect = 0.0
 Identities = 325/552 (58%), Positives = 415/552 (75%), Gaps = 10/552 (1%)

Query: 25  EAEAKKWIDSEFQPSTLNKDQQMAEMKWFIDAAKKLQAKGVKEISVVSETITTHEYESKT 84
           +++ +  I+  F  STL+ D+Q  E+ WF  AA +L+     EISV+SE + TH+YE++ 
Sbjct: 43  QSQIRTLIEDHFPDSTLSADEQAEELAWFAHAASELKGT---EISVLSEQLPTHDYEAEV 99

Query: 85  LAKAFEEITGIKVKHDLIQEGDVVEKLQTS-MQSGKSIYDGWISDSDLIGTHYRYGKIMN 143
           LA AF E+T I V HD   EG+V+ ++    + + K  YD +++DSD+IGTH R G  + 
Sbjct: 100 LAPAFSELTEIPVTHDRRPEGEVIRQINLQRIMAAKGRYDAFVNDSDMIGTHSRSGWALA 159

Query: 144 LTDYMGGAGKEWTNPGIDLKDYIGTKFTTGPDGKLYQLPDQQFANLYWFRADLFDRKDIK 203
           L+DYM GAG+ +T P + L+D+IG +F TGPDGK+YQLPDQQFANLYWFR D F R +++
Sbjct: 160 LSDYMEGAGEAFTLPTLSLEDFIGLEFVTGPDGKMYQLPDQQFANLYWFRYDWFQRPELR 219

Query: 204 DKFKAKYGYDLGVPLNWSAYEDIAEFFTNDVKNIDGKPIYGHMDYGKKDPSLGWRFTDAW 263
            +F  +YGY+LGVP+NWSAYEDIAEFFT  V+ IDG+ +YGHMDYGK+DPSLGWRFTDAW
Sbjct: 220 VRFMERYGYELGVPVNWSAYEDIAEFFTVHVREIDGERVYGHMDYGKRDPSLGWRFTDAW 279

Query: 264 LSMAGTADIGAPNGLPIDEWGIRVADDKCTPVGASVARGGATNSPAAVYALTKYVDWMKK 323
            SMAG  D G PNGLP+DEWGIR+  + C PVG+SV+RGGATNSPAAVYAL KY+DW+++
Sbjct: 280 FSMAGAGDRGIPNGLPVDEWGIRM--EGCHPVGSSVSRGGATNSPAAVYALAKYIDWLQR 337

Query: 324 YAPKEATGMTFGEAGPVPAQGQIAQQIFWYTAFTADMTKPGLPVVNADGTPKWRMAPGPN 383
           +AP EA  MTF EAGPVPA+GQ+AQQIFWYTAFT+DM K GLPVVN DGTPKWRMAP P 
Sbjct: 338 FAPPEAANMTFSEAGPVPARGQVAQQIFWYTAFTSDMAKEGLPVVNEDGTPKWRMAPSPR 397

Query: 384 GPYWKQGMQNGYQDVGSWTFFKDHDANKTAAAWLYAQFVTAKTTSLKKTMVGLTPIRESD 443
           G YW++GM+ GYQDVG+WT  +   +N+  AAWLYAQF  ++T SL+KT+ GLTPIR SD
Sbjct: 398 GAYWQEGMKLGYQDVGAWTIPRAMGSNQQKAAWLYAQFTVSRTVSLQKTLYGLTPIRLSD 457

Query: 444 IQSKAMTDMAPKLGGLVEFYRSPARVAWSPTGTNVPDYPKLAQLWWKNVAQAVTGEKTPQ 503
           ++S  M + AP LGGLVEFYRSPAR AWSPTG NVPDYP+LA+LWW N+A AVTG+ TPQ
Sbjct: 458 LESPQMQEKAPTLGGLVEFYRSPARTAWSPTGVNVPDYPRLAKLWWPNIADAVTGKVTPQ 517

Query: 504 GAMDTLADEMDQVMARLERAGMA-HCAPKLNAK---SDPNKWLSDKQAPWKKLANEKPKG 559
            A+D LA   D+ ++ +ER  +A  C PK+  +    D + WL+   AP  +L NEKP G
Sbjct: 518 QALDNLAAAQDRTLSVIERNFLAGDCGPKMAKEEQLKDADWWLAQPGAPKPRLRNEKPPG 577

Query: 560 ETIAYGTLLQAW 571
           +TI Y  LL+ W
Sbjct: 578 KTIRYEDLLKQW 589


Lambda     K      H
   0.315    0.132    0.412 

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: 1233
Number of extensions: 58
Number of successful extensions: 5
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: 594
Length adjustment: 37
Effective length of query: 540
Effective length of database: 557
Effective search space:   300780
Effective search space used:   300780
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: 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