Aligments for a candidate for kguT in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for kguT in Pseudomonas putida KT2440

Align KguT (characterized, see rationale)
to candidate PP_3377 PP_3377 2-ketogluconate transporter, putative

Query= uniprot:A0A167V864
         (425 letters)



>lcl|FitnessBrowser__Putida:PP_3377 PP_3377 2-ketogluconate
           transporter, putative
          Length = 430

 Score =  762 bits (1968), Expect = 0.0
 Identities = 366/418 (87%), Positives = 390/418 (93%)

Query: 1   MQIDRLAPRRWWYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFL 60
           MQ   LAPRRWWYI+PIVF+TYSLAYLDRANYGFAAASGMA+DLHITP LSSLLGALFFL
Sbjct: 1   MQSQSLAPRRWWYIIPIVFVTYSLAYLDRANYGFAAASGMAEDLHITPVLSSLLGALFFL 60

Query: 61  GYFFFQVPGAIYAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVM 120
           GYFFFQVPGAIYAEKRSVKKLIFV LILWGGLATLTGMV +V +LI IRFLLGVVEAAVM
Sbjct: 61  GYFFFQVPGAIYAEKRSVKKLIFVCLILWGGLATLTGMVSNVYMLIGIRFLLGVVEAAVM 120

Query: 121 PAMLIYLCHWFTRAERSRANTFLILGNPVTILWMSVVSGYLVKHFDWRWMFIIEGLPAVL 180
           PAML+YLCHWFTRAERSRANTFL+LGNPVTILWMSVVSGYL+KH+DWRWMFIIEGLPAV+
Sbjct: 121 PAMLVYLCHWFTRAERSRANTFLMLGNPVTILWMSVVSGYLIKHYDWRWMFIIEGLPAVI 180

Query: 181 WAFIWWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQY 240
           WAF WWRLVDDRP Q +WL  QEK AL +ALAAEQQGIKPVKNYREAFRSP+VIIL+LQY
Sbjct: 181 WAFFWWRLVDDRPAQVAWLSEQEKAALAQALAAEQQGIKPVKNYREAFRSPQVIILALQY 240

Query: 241 FCWSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRF 300
           FCWSIGVYGFVLWLPSILKQAA +DIV AGWL++VPYL AVLAM+GVSWASDR+QKRKRF
Sbjct: 241 FCWSIGVYGFVLWLPSILKQAANVDIVQAGWLASVPYLAAVLAMVGVSWASDRLQKRKRF 300

Query: 301 VWPPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGA 360
           VWPPLLIAALAFYGSY LG+EHFW SY LLV+AGACMYAPYGPFFAIVPE+LP+NVAGGA
Sbjct: 301 VWPPLLIAALAFYGSYALGSEHFWLSYALLVVAGACMYAPYGPFFAIVPEILPANVAGGA 360

Query: 361 MALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQARR 418
           MALINSMGALGSF GSWLVGYLNG TGGPGASYLFMCGALL AVALTA LN SQ + R
Sbjct: 361 MALINSMGALGSFGGSWLVGYLNGATGGPGASYLFMCGALLTAVALTAALNTSQTSGR 418


Lambda     K      H
   0.328    0.140    0.457 

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: 896
Number of extensions: 41
Number of successful extensions: 2
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: 425
Length of database: 430
Length adjustment: 32
Effective length of query: 393
Effective length of database: 398
Effective search space:   156414
Effective search space used:   156414
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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