Alignments for a candidate for lctP in Halococcus hamelinensis 100A6

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Halococcus hamelinensis 100A6

Align L-lactate permease (characterized, see rationale)
to candidate WP_007690279.1 C447_RS01800 L-lactate permease

Query= uniprot:A0KZB2
         (547 letters)



>NCBI__GCF_000336675.1:WP_007690279.1
          Length = 571

 Score =  343 bits (880), Expect = 1e-98
 Identities = 192/561 (34%), Positives = 308/561 (54%), Gaps = 21/561 (3%)

Query: 3   ILQLLASLTPVISVMIFLVLLRMPASKAMPISMIITALAAVFIWQMDTTLLAASVLEGLL 62
           I  +L ++ P++++ + +V L  PA++AMP++ ++   A V  W M    +AA+ + G +
Sbjct: 4   IAGVLVAVLPLVAIAVLMVGLFWPATRAMPVAWLVAVAAGVVGWGMSPRWVAAATINGFI 63

Query: 63  SAITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSAGF 122
           +A   L I+FGA+ LL TLK +GA D I  GF  +S D RVQV+++ +L G+FIEG+AGF
Sbjct: 64  TATQILWIVFGAILLLYTLKQTGAFDAISGGFAAVSDDRRVQVVLLVFLMGSFIEGAAGF 123

Query: 123 GTPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLTQGGVSLAAE 182
           GTPAA+  PLLV LG PP+AA VVAL  +   ++FGA+G P++ G+ Q       ++   
Sbjct: 124 GTPAAVVGPLLVGLGFPPLAAVVVALTGNLMAITFGAVGTPLIIGL-QDTFASSEAIRTT 182

Query: 183 QFAAHGGSYVGYARFIVMHMITIDLITGTLIPLVMVTILTGFFGRNKSFKEGLAIWKFAI 242
             A    +   +   I     T  +I G  +P + V ++T FFG  +S +  L +    +
Sbjct: 183 VTAETPYTIASWVAEIGAWAATYHVIVGIAVPFIGVAMMTRFFGAERSVRPALEVLPLCL 242

Query: 243 FAGLAFTVPAWIINYLAGPEFPSVIGSLVGMALVIPVARKGYLLPKTPWN---------- 292
           F+  +F VP W+     GP FP ++G++VG+AL + V R GYL P   W           
Sbjct: 243 FSWASFAVPYWLTAMFLGPVFPGLVGAMVGLALTVGVLRLGYLHPDEEWEFDDRSAWPDH 302

Query: 293 -----DFAENDSQEGAKIE---TTAKFSQIAAWTPYIIMAALLVLSRTVAPLKAWLSSFN 344
                +  E+ ++ GA      T        AW PY ++  +LV +RT+ P+ ++L +  
Sbjct: 303 WVGEIEPGESSNRSGAIAADGGTAQAMPLWKAWAPYALLVVVLVATRTIDPIASFLQANG 362

Query: 345 I-SWTGLMGTELKASFATLYAPGAFFVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTII 403
           +  W+ ++GT L    A LY PGA FV V +L     +M    ++ +   + + + P ++
Sbjct: 363 VLVWSDILGTGLTNDVAVLYLPGAAFVLVSLLTVGFHRMSGDEVRGAWRETGEKIAPPVV 422

Query: 404 SLGASVPMVKIFLNSGVNGAGLASMPVALADMLGQSMGAVWAWMAPIVGIFGAFLSGSAT 463
           +L  +V  V++ L SG    G  SM + L+       G ++ + AP+VG  GAFL+GS T
Sbjct: 423 ALLFAVATVQVMLQSGA-ATGSDSMLIVLSQATADLAGGIYPFFAPLVGALGAFLAGSNT 481

Query: 464 FSNMMFSSLQYSVADNIGMNHTLVLALQGIGANAGNMMCVMNVVAAATVVGMAGRESEII 523
            S+++F + QY VA +I  + T++L  Q +G   GN++ V NVVAA  VVG+ G E  +I
Sbjct: 482 VSDILFGTFQYGVATDIETSRTIMLGAQAVGGAIGNLIAVHNVVAALAVVGLVGEEGRVI 541

Query: 524 RKTMPVAIGYALLAGTIATLW 544
           R  +     YA  AG ++ L+
Sbjct: 542 RLELIPLAYYAAFAGLLSLLF 562


Lambda     K      H
   0.326    0.138    0.413 

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: 957
Number of extensions: 49
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: 547
Length of database: 571
Length adjustment: 36
Effective length of query: 511
Effective length of database: 535
Effective search space:   273385
Effective search space used:   273385
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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:

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