Aligments for a candidate for glpV in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Aligments for a candidate for glpV in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for Glycerol, periplasmic substrate-binding component (characterized)
to candidate AO356_21635 AO356_21635 ABC transporter substrate-binding protein

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_21635
          Length = 580

 Score =  842 bits (2174), Expect = 0.0
 Identities = 400/569 (70%), Positives = 465/569 (81%), Gaps = 8/569 (1%)

Query: 7   AIAFAAAALAMGQAAWAGEAE--AKKWIDSEFQPSTLNKDQQMAEMKWFIDAAKKLQAKG 64
           ++A   A   +   AWA   E  AKKWI SEF+PSTL  +QQ+ E+KWFI AA+    +G
Sbjct: 13  SLAAMLALSGLSATAWADAYEDAAKKWIGSEFKPSTLTAEQQLEELKWFIKAAQPF--RG 70

Query: 65  VKEISVVSETITTHEYESKTLAKAFEEITGIKVKHDLIQEGDVVEKLQTSMQSGKSIYDG 124
           +K I+VVSETI THEYESK LAKAF EITGI++ HDL+QEGDVVEKLQT MQS K+IYDG
Sbjct: 71  MK-INVVSETIATHEYESKVLAKAFTEITGIQLTHDLLQEGDVVEKLQTQMQSDKNIYDG 129

Query: 125 WISDSDLIGTHYRYGKIMNLTDYMGGAGKEWTNPGIDLKDYIGTKFTTGPDGKLYQLPDQ 184
           W++DSDLIGTH+RYGK  ++TD M   GK++T+P +DLKD+IG  FTT PDGK+YQLPDQ
Sbjct: 130 WVNDSDLIGTHFRYGKTESITDLMANEGKDFTSPTLDLKDFIGISFTTAPDGKVYQLPDQ 189

Query: 185 QFANLYWFRADLFDRKDIKDKFKAKYGYDLGVPLNWSAYEDIAEFFTNDVKNIDGKPIYG 244
           QFANLYWFRAD F+R D+K KFK KYGY+LGVP+NWSAYEDIA+FF+ DVK IDGK +YG
Sbjct: 190 QFANLYWFRADWFERADLKAKFKEKYGYELGVPVNWSAYEDIAKFFSEDVKEIDGKRVYG 249

Query: 245 HMDYGKKDPSLGWRFTDAWLSMAGTADIGAPNGLPIDEWGIRVADDKCTPVGASVARGGA 304
           HMDYGKKDPSLGWRFTDAW SMAG  D G PNGLP+DEWGIRV D  C PVG+SV RGG 
Sbjct: 250 HMDYGKKDPSLGWRFTDAWFSMAGGGDKGLPNGLPVDEWGIRVED--CHPVGSSVTRGGD 307

Query: 305 TNSPAAVYALTKYVDWMKKYAPKEATGMTFGEAGPVPAQGQIAQQIFWYTAFTADMTKPG 364
           TN PAAV+A TKYVDWMKKYAP EA GMTF E+GPVP+QG IAQQIFWYTAFTADMTKPG
Sbjct: 308 TNGPAAVFATTKYVDWMKKYAPPEAAGMTFSESGPVPSQGNIAQQIFWYTAFTADMTKPG 367

Query: 365 LPVVNADGTPKWRMAPGPNGPYWKQGMQNGYQDVGSWTFFKDHDANKTAAAWLYAQFVTA 424
           LPV+NADGTPKWRMAP P GPYW++GM+ GYQDVGSWTF K     +  AAWLYAQFVT+
Sbjct: 368 LPVMNADGTPKWRMAPSPRGPYWEEGMKLGYQDVGSWTFMKSTPEKQKLAAWLYAQFVTS 427

Query: 425 KTTSLKKTMVGLTPIRESDIQSKAMTDMAPKLGGLVEFYRSPARVAWSPTGTNVPDYPKL 484
           KT SLKKT+VGLTPIRESDI S+A+TD+APKLGGLVEFYRSPARV W+PTGTNVPDYP+L
Sbjct: 428 KTVSLKKTIVGLTPIRESDINSQALTDLAPKLGGLVEFYRSPARVQWTPTGTNVPDYPRL 487

Query: 485 AQLWWKNVAQAVTGEKTPQGAMDTLADEMDQVMARLERA-GMAHCAPKLNAKSDPNKWLS 543
           AQLWW ++A+A +GEKTPQ A+D LA + D +M RLER+   A CAPK+N + D   W  
Sbjct: 488 AQLWWSHIAEAASGEKTPQQALDGLAKDQDAIMTRLERSKAQATCAPKMNPERDAQYWFD 547

Query: 544 DKQAPWKKLANEKPKGETIAYGTLLQAWK 572
              AP  KLANEKPKGET++Y  LL++W+
Sbjct: 548 QPGAPKPKLANEKPKGETVSYTELLKSWE 576


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: 1316
Number of extensions: 67
Number of successful extensions: 4
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: 580
Length adjustment: 36
Effective length of query: 541
Effective length of database: 544
Effective search space:   294304
Effective search space used:   294304
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.

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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, or view the source code.

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