Aligments for a candidate for lctP in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Aligments for a candidate for lctP in Shewanella sp. ANA-3

Align L-lactate permease (characterized, see rationale)
to candidate 7025754 Shewana3_2904 L-lactate permease (RefSeq)

Query= uniprot:Q8EGS2
         (547 letters)



>FitnessBrowser__ANA3:7025754
          Length = 547

 Score = 1028 bits (2658), Expect = 0.0
 Identities = 521/547 (95%), Positives = 539/547 (98%)

Query: 1   MTILQLFASLTPVLSVMIFLVLLRMPASKAMPISMVVTAIAAVFIWQMDTTLLAASVVEG 60
           MTILQL ASLTPV+SVMIFLVLLRMPASKAMPISM++TA+AAVFIWQMDTTLLAASV+EG
Sbjct: 1   MTILQLLASLTPVISVMIFLVLLRMPASKAMPISMIITALAAVFIWQMDTTLLAASVLEG 60

Query: 61  LLSAITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSA 120
           LLSAITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSA
Sbjct: 61  LLSAITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSA 120

Query: 121 GFGTPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLIQGGVSMA 180
           GFGTPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGL QGGVS+A
Sbjct: 121 GFGTPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLTQGGVSLA 180

Query: 181 AEQFAAHGGTYAGYARYIVMHMITIDLITGTLIPLVMVTMLTGFFGRNKSFKEGLAIWKF 240
           AEQFAAHGG+Y GYAR+IVMHMITIDLITGTLIPLVMVT+LTGFFGRNKSFKEGLAIWKF
Sbjct: 181 AEQFAAHGGSYVGYARFIVMHMITIDLITGTLIPLVMVTILTGFFGRNKSFKEGLAIWKF 240

Query: 241 AIFSGLAFTVPAWIINYLAGPEFPSVIGALIGMAMVIPVARKGYLLPKTPWNDFAENDNQ 300
           AIF+GLAFTVPAWIINYLAGPEFPSVIG+L+GMA+VIPVARKGYLLPKTPWNDFAEND+Q
Sbjct: 241 AIFAGLAFTVPAWIINYLAGPEFPSVIGSLVGMALVIPVARKGYLLPKTPWNDFAENDSQ 300

Query: 301 DGVKLETTAKFSQIAAWTPYIIMAALLVLSRTVAPLKAWLSGFNINWTGLLGTELKASFA 360
           +G K+ETTAKFSQIAAWTPYIIMAALLVLSRTVAPLKAWLS FNI+WTGL+GTELKASFA
Sbjct: 301 EGAKIETTAKFSQIAAWTPYIIMAALLVLSRTVAPLKAWLSSFNISWTGLMGTELKASFA 360

Query: 361 TLYAPGAFFVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIISLGASVPMVKIFLNSGA 420
           TLYAPGAFFVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIISLGASVPMVKIFLNSG 
Sbjct: 361 TLYAPGAFFVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIISLGASVPMVKIFLNSGV 420

Query: 421 NGAGLASMPVALADMLASSMGAVWAWMAPIVGIFGAFLSGSATFSNMMFSSLQYSVADNI 480
           NGAGLASMPVALADML  SMGAVWAWMAPIVGIFGAFLSGSATFSNMMFSSLQYSVADNI
Sbjct: 421 NGAGLASMPVALADMLGQSMGAVWAWMAPIVGIFGAFLSGSATFSNMMFSSLQYSVADNI 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: 1229
Number of extensions: 41
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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