Alignments for a candidate for glpV in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpV in Pseudomonas putida KT2440

Align ABC transporter for Glycerol, periplasmic substrate-binding component (characterized)
to candidate PP_2264 PP_2264 putative Sugar ABC transporter, periplasmic sugar-binding protein

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



>FitnessBrowser__Putida:PP_2264
          Length = 579

 Score =  841 bits (2172), Expect = 0.0
 Identities = 398/555 (71%), Positives = 461/555 (83%), Gaps = 8/555 (1%)

Query: 21  AWAGEAE--AKKWIDSEFQPSTLNKDQQMAEMKWFIDAAKKLQAKGVKEISVVSETITTH 78
           AWA + E  AKKWI SEF+PSTL  +QQ+AE++WFI AA+    +G+K I+VVSETITTH
Sbjct: 26  AWADQYEEAAKKWIGSEFKPSTLTPEQQLAELQWFIKAAEPF--RGMK-INVVSETITTH 82

Query: 79  EYESKTLAKAFEEITGIKVKHDLIQEGDVVEKLQTSMQSGKSIYDGWISDSDLIGTHYRY 138
           EYESK LAKAF EITGI++ HDL+QEGDVVEKLQT MQS K+IYDGW++DSDLIGTH+RY
Sbjct: 83  EYESKVLAKAFSEITGIQLTHDLLQEGDVVEKLQTQMQSDKNIYDGWVNDSDLIGTHFRY 142

Query: 139 GKIMNLTDYMGGAGKEWTNPGIDLKDYIGTKFTTGPDGKLYQLPDQQFANLYWFRADLFD 198
           GK+ ++TD M   GK +T+P +DLKD+IG  FTT PDGK+YQLPDQQFANLYWFRAD F+
Sbjct: 143 GKVESITDLMANEGKAYTSPTLDLKDFIGISFTTAPDGKVYQLPDQQFANLYWFRADWFE 202

Query: 199 RKDIKDKFKAKYGYDLGVPLNWSAYEDIAEFFTNDVKNIDGKPIYGHMDYGKKDPSLGWR 258
           R ++K +FK KYGY+LGVP+NWSAYEDIA+FFT DVK IDGK +YGHMDYGKKDPSLGWR
Sbjct: 203 RPELKARFKEKYGYELGVPVNWSAYEDIAKFFTEDVKEIDGKRVYGHMDYGKKDPSLGWR 262

Query: 259 FTDAWLSMAGTADIGAPNGLPIDEWGIRVADDKCTPVGASVARGGATNSPAAVYALTKYV 318
           FTDAW SMAG  D G PNGLP+DEWGIRV D  C PVG+SV RGG TN PAAVYA  KYV
Sbjct: 263 FTDAWFSMAGGGDKGLPNGLPVDEWGIRVED--CHPVGSSVTRGGDTNGPAAVYATQKYV 320

Query: 319 DWMKKYAPKEATGMTFGEAGPVPAQGQIAQQIFWYTAFTADMTKPGLPVVNADGTPKWRM 378
           DWM+ YAPKEA GMTF EAGPVPAQG IAQQIFWYTAFTADMTKPGLPVVNADGTPKWRM
Sbjct: 321 DWMRAYAPKEAQGMTFSEAGPVPAQGNIAQQIFWYTAFTADMTKPGLPVVNADGTPKWRM 380

Query: 379 APGPNGPYWKQGMQNGYQDVGSWTFFKDHDANKTAAAWLYAQFVTAKTTSLKKTMVGLTP 438
           AP P GPYW++GM+ GYQD GSWTFFK     +  AAWLYAQFVT+KT SLKKT+VGLTP
Sbjct: 381 APSPKGPYWEEGMKLGYQDTGSWTFFKSTPEKQRLAAWLYAQFVTSKTVSLKKTIVGLTP 440

Query: 439 IRESDIQSKAMTDMAPKLGGLVEFYRSPARVAWSPTGTNVPDYPKLAQLWWKNVAQAVTG 498
           IRESDI S+AMT++APKLGGLVEFYRSPARV W+PTGTNVPDYP+LAQLWW ++A+  +G
Sbjct: 441 IRESDINSQAMTELAPKLGGLVEFYRSPARVQWTPTGTNVPDYPRLAQLWWSHIAEVASG 500

Query: 499 EKTPQGAMDTLADEMDQVMARLERA-GMAHCAPKLNAKSDPNKWLSDKQAPWKKLANEKP 557
           EKTPQ A+D LA + D++M RL+R+   A CAPKLN + D   W     AP  KLANEKP
Sbjct: 501 EKTPQEALDGLARDQDRMMERLQRSNAQATCAPKLNPEKDAQYWFDQPGAPKAKLANEKP 560

Query: 558 KGETIAYGTLLQAWK 572
            GET++Y  LL++W+
Sbjct: 561 MGETVSYNELLKSWE 575


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: 1315
Number of extensions: 67
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: 579
Length adjustment: 36
Effective length of query: 541
Effective length of database: 543
Effective search space:   293763
Effective search space used:   293763
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)
SQLite3 databases

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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