GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctP in Shewanella oneidensis MR-1

Align L-lactate permease (characterized, see rationale)
to candidate 200693 SO1522 L-lactate permease, putative (NCBI ptt file)

Query= uniprot:Q8EGS2
         (547 letters)



>FitnessBrowser__MR1:200693
          Length = 547

 Score = 1062 bits (2747), Expect = 0.0
 Identities = 547/547 (100%), Positives = 547/547 (100%)

Query: 1   MTILQLFASLTPVLSVMIFLVLLRMPASKAMPISMVVTAIAAVFIWQMDTTLLAASVVEG 60
           MTILQLFASLTPVLSVMIFLVLLRMPASKAMPISMVVTAIAAVFIWQMDTTLLAASVVEG
Sbjct: 1   MTILQLFASLTPVLSVMIFLVLLRMPASKAMPISMVVTAIAAVFIWQMDTTLLAASVVEG 60

Query: 61  LLSAITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSA 120
           LLSAITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSA
Sbjct: 61  LLSAITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSA 120

Query: 121 GFGTPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLIQGGVSMA 180
           GFGTPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLIQGGVSMA
Sbjct: 121 GFGTPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLIQGGVSMA 180

Query: 181 AEQFAAHGGTYAGYARYIVMHMITIDLITGTLIPLVMVTMLTGFFGRNKSFKEGLAIWKF 240
           AEQFAAHGGTYAGYARYIVMHMITIDLITGTLIPLVMVTMLTGFFGRNKSFKEGLAIWKF
Sbjct: 181 AEQFAAHGGTYAGYARYIVMHMITIDLITGTLIPLVMVTMLTGFFGRNKSFKEGLAIWKF 240

Query: 241 AIFSGLAFTVPAWIINYLAGPEFPSVIGALIGMAMVIPVARKGYLLPKTPWNDFAENDNQ 300
           AIFSGLAFTVPAWIINYLAGPEFPSVIGALIGMAMVIPVARKGYLLPKTPWNDFAENDNQ
Sbjct: 241 AIFSGLAFTVPAWIINYLAGPEFPSVIGALIGMAMVIPVARKGYLLPKTPWNDFAENDNQ 300

Query: 301 DGVKLETTAKFSQIAAWTPYIIMAALLVLSRTVAPLKAWLSGFNINWTGLLGTELKASFA 360
           DGVKLETTAKFSQIAAWTPYIIMAALLVLSRTVAPLKAWLSGFNINWTGLLGTELKASFA
Sbjct: 301 DGVKLETTAKFSQIAAWTPYIIMAALLVLSRTVAPLKAWLSGFNINWTGLLGTELKASFA 360

Query: 361 TLYAPGAFFVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIISLGASVPMVKIFLNSGA 420
           TLYAPGAFFVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIISLGASVPMVKIFLNSGA
Sbjct: 361 TLYAPGAFFVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIISLGASVPMVKIFLNSGA 420

Query: 421 NGAGLASMPVALADMLASSMGAVWAWMAPIVGIFGAFLSGSATFSNMMFSSLQYSVADNI 480
           NGAGLASMPVALADMLASSMGAVWAWMAPIVGIFGAFLSGSATFSNMMFSSLQYSVADNI
Sbjct: 421 NGAGLASMPVALADMLASSMGAVWAWMAPIVGIFGAFLSGSATFSNMMFSSLQYSVADNI 480

Query: 481 GMNHTLVLALQGIGANAGNMMCVMNVVAAATVVGMAGRESEIIRKTMPVAIGYALLAGTI 540
           GMNHTLVLALQGIGANAGNMMCVMNVVAAATVVGMAGRESEIIRKTMPVAIGYALLAGTI
Sbjct: 481 GMNHTLVLALQGIGANAGNMMCVMNVVAAATVVGMAGRESEIIRKTMPVAIGYALLAGTI 540

Query: 541 ATLWGGF 547
           ATLWGGF
Sbjct: 541 ATLWGGF 547


Lambda     K      H
   0.326    0.138    0.415 

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: 1275
Number of extensions: 43
Number of successful extensions: 3
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: 547
Length of database: 547
Length adjustment: 36
Effective length of query: 511
Effective length of database: 511
Effective search space:   261121
Effective search space used:   261121
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: 52 (24.6 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