GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpV in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for Glycerol, periplasmic substrate-binding component (characterized)
to candidate Pf1N1B4_4013 Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4013
          Length = 580

 Score =  842 bits (2174), Expect = 0.0
 Identities = 398/569 (69%), Positives = 460/569 (80%), Gaps = 8/569 (1%)

Query: 7   AIAFAAAALAMGQAAWAGEAE--AKKWIDSEFQPSTLNKDQQMAEMKWFIDAAKKLQAKG 64
           ++A   A   +  AAWA   E  AKKWI SEF+PSTL + QQ+ E+KWFI A++  +   
Sbjct: 13  SLAAMLALSGLSAAAWADAYEDAAKKWIGSEFKPSTLTEAQQLEELKWFIKASEPFRGMS 72

Query: 65  VKEISVVSETITTHEYESKTLAKAFEEITGIKVKHDLIQEGDVVEKLQTSMQSGKSIYDG 124
           +K   VVSETI THEYESKTLAKAF EITGIK+ HDL+QEGDVVEKLQT MQS K+IYDG
Sbjct: 73  IK---VVSETIATHEYESKTLAKAFTEITGIKLTHDLLQEGDVVEKLQTQMQSDKNIYDG 129

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

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

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

Query: 305 TNSPAAVYALTKYVDWMKKYAPKEATGMTFGEAGPVPAQGQIAQQIFWYTAFTADMTKPG 364
           TN PAAVYA TKYVDWMKKYAP EA GMTF E+GPVP+QG IAQQIFWYTAFTADMTKPG
Sbjct: 308 TNGPAAVYATTKYVDWMKKYAPPEAAGMTFSESGPVPSQGNIAQQIFWYTAFTADMTKPG 367

Query: 365 LPVVNADGTPKWRMAPGPNGPYWKQGMQNGYQDVGSWTFFKDHDANKTAAAWLYAQFVTA 424
           LPV+NADGTPKWRMAP P GPYW++GM+ GYQD GSWTF K     +  AAWLYAQFVT+
Sbjct: 368 LPVMNADGTPKWRMAPSPKGPYWEEGMKLGYQDAGSWTFLKSTPEKQKLAAWLYAQFVTS 427

Query: 425 KTTSLKKTMVGLTPIRESDIQSKAMTDMAPKLGGLVEFYRSPARVAWSPTGTNVPDYPKL 484
           KT SLKKT+VGLTPIRESDI S+AMTD+APKLGGLVEFYRSPARV W+PTGTNVPDYP+L
Sbjct: 428 KTVSLKKTIVGLTPIRESDINSQAMTDLAPKLGGLVEFYRSPARVQWTPTGTNVPDYPRL 487

Query: 485 AQLWWKNVAQAVTGEKTPQGAMDTLADEMDQVMARLERAGM-AHCAPKLNAKSDPNKWLS 543
           AQLWW ++A+A +GEKTPQ A+D LA + D +M RLER+ +   C PK+N + D   W  
Sbjct: 488 AQLWWSHIAEAASGEKTPQQALDGLAKDQDAIMTRLERSKVQPTCGPKMNPERDAQYWFD 547

Query: 544 DKQAPWKKLANEKPKGETIAYGTLLQAWK 572
              AP  KLANEKPKGET++Y  LL++W+
Sbjct: 548 QPGAPKAKLANEKPKGETVSYAELLKSWE 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: 1321
Number of extensions: 68
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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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:

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:

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:

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:

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