Alignments for a candidate for glt in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for glt in Klebsiella michiganensis M5al

Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate BWI76_RS02105 BWI76_RS02105 glutamate/aspartate:proton symporter GltP

Query= SwissProt::P21345
         (437 letters)



>FitnessBrowser__Koxy:BWI76_RS02105
          Length = 437

 Score =  779 bits (2012), Expect = 0.0
 Identities = 402/434 (92%), Positives = 421/434 (97%)

Query: 2   KNIKFSLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIVI 61
           K  K S+AWQIL A+VLGILLGSYLHYH++SRDWL+ NLL+PAGDIFIHLIKMIVVPIVI
Sbjct: 3   KKTKVSMAWQILLALVLGILLGSYLHYHAESRDWLISNLLTPAGDIFIHLIKMIVVPIVI 62

Query: 62  STLVVGIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAGVDMSQLATVD 121
           STLVVGIAGVGDAKQLGRIGAKTIIYFEVITTVAI+LGITLANVFQPG+G+DMSQLA VD
Sbjct: 63  STLVVGIAGVGDAKQLGRIGAKTIIYFEVITTVAIVLGITLANVFQPGSGIDMSQLAAVD 122

Query: 122 ISKYQSTTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPATH 181
           ISKYQ+TT  VQS +HG+MGTILSLVPTNIVASMAKG+MLPIIFFSVLFGLGLSSLPATH
Sbjct: 123 ISKYQNTTAEVQSHAHGLMGTILSLVPTNIVASMAKGDMLPIIFFSVLFGLGLSSLPATH 182

Query: 182 REPLVTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFAI 241
           REPLVTVFRSISETMFKVTHMVMRYAPVGVFALI+VTVA FGF+SLWPLAKLV+LV+FAI
Sbjct: 183 REPLVTVFRSISETMFKVTHMVMRYAPVGVFALISVTVATFGFASLWPLAKLVILVYFAI 242

Query: 242 LFFALVVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSIT 301
           LFFALVVLGIVAR+CGLS+W LIRILKDELILAYSTASSESVLPRIIEKMEAYGAP SIT
Sbjct: 243 LFFALVVLGIVARVCGLSIWTLIRILKDELILAYSTASSESVLPRIIEKMEAYGAPASIT 302

Query: 302 SFVVPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGVS 361
           SFVVPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEI LVLTLMVTSKGIAGVPGVS
Sbjct: 303 SFVVPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEITLVLTLMVTSKGIAGVPGVS 362

Query: 362 FVVLLATLGSVGIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKKAL 421
           FVVLLATLGSVGIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKKAL
Sbjct: 363 FVVLLATLGSVGIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKKAL 422

Query: 422 AYEREVLGKFDKTA 435
           AYEREVLGKFDKTA
Sbjct: 423 AYEREVLGKFDKTA 436


Lambda     K      H
   0.326    0.141    0.403 

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: 766
Number of extensions: 23
Number of successful extensions: 1
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: 437
Length of database: 437
Length adjustment: 32
Effective length of query: 405
Effective length of database: 405
Effective search space:   164025
Effective search space used:   164025
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 (21.7 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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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