Alignments for a candidate for lctP in Bacillus altitudinis 41KF2b

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Bacillus altitudinis 41KF2b

Align L-lactate permease (characterized)
to candidate WP_035703106.1 BA79_RS12640 L-lactate permease

Query= SwissProt::P33231
         (551 letters)



>NCBI__GCF_000691145.1:WP_035703106.1
          Length = 540

 Score =  517 bits (1332), Expect = e-151
 Identities = 270/542 (49%), Positives = 376/542 (69%), Gaps = 6/542 (1%)

Query: 3   LWQQNYDPAGNIWLSSLIASLPILFFFFALIKLKLKGYVAASWTVAIALAVALLFYKMPV 62
           +WQQ YDP GN ++S+L+A LPILFF  AL   KLKG +AA +T+ ++   A+ F+ MP+
Sbjct: 1   MWQQIYDPFGNEFVSALVAMLPILFFLLALTVFKLKGVLAACFTLIVSFVTAVFFFHMPI 60

Query: 63  ANALASVVYGFFYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITPDQRLQMLIVG 122
             AL++VV G   GLWPI +I+I AV++YKI+VK+G+FD+IRSSI  I+ DQRLQ+L++G
Sbjct: 61  EKALSAVVLGVSNGLWPIGYIVIMAVWLYKIAVKSGKFDVIRSSIAGISKDQRLQLLLIG 120

Query: 123 FCFGAFLEGAAGFGAPVAITAALLVGLGFKPLYAAGLCLIVNTAPVAFGAMGIPILVAGQ 182
           F F AFLEGAAGFG P+AI+AALL  LGFKPL AA LCLI N A  AFGA+GIP++   Q
Sbjct: 121 FSFNAFLEGAAGFGVPIAISAALLTELGFKPLKAAMLCLIANAASGAFGAVGIPVITGAQ 180

Query: 183 VTGIDSFEIGQMVGRQLPFMTIIVLFWIMAIMDGWRGIKETWPAVVVAGGSFAIAQYLSS 242
           +  +   E+ Q +   +PF++  + F ++ I+DG++GIKET PA++V  GS+AI Q ++ 
Sbjct: 181 MGNMTPLELSQTLVYTIPFISFCIPFLLILIVDGFKGIKETLPALLVVSGSYAILQAVTM 240

Query: 243 NFIGPELPDIISSLVSLLCLTLFLKRWQPVRVFRFGDLGASQVDMTLAHTGYTAGQVLRA 302
             +GPEL +IIS+L S+  L LFL++WQP  ++R  + GA  ++     +G    +VL+A
Sbjct: 241 VTMGPELANIISALASMGILALFLRKWQPKHIYR--EEGAPAIEQKQTFSGV---EVLKA 295

Query: 303 WTPFLFLTATVTLWSIPPFKALFASGGALYEWVINIPVPYLDKLVARMPPVVSEATAYAA 362
           W+PF  LTA +T+WS+P FKALFA GG L    I + +P+L + + ++PP+    T   A
Sbjct: 296 WSPFYILTAVITVWSLPAFKALFAVGGPLNWTTILVKMPFLHQQIVKLPPIAQTETPIDA 355

Query: 363 VFKFDWFSATGTAILFAALLSIVWLK-MKPSDAISTFGSTLKELALPIYSIGMVLAFAFI 421
           +FK D  SATGTAIL A +L+ ++ + +   +  +   + +KEL +P+ +I  V+ FA +
Sbjct: 356 IFKIDVISATGTAILIAVMLTGLFSRHITLKEGAACLNAAVKELWVPVLTICFVMGFANL 415

Query: 422 SNYSGLSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQIGVS 481
           +N++GLSS + LALA TG  F   SP LGW+GVF+TGS  S+NALF  LQA  A QIG  
Sbjct: 416 ANFAGLSSAIGLALAKTGDLFPLVSPVLGWIGVFITGSVVSNNALFGNLQAVTASQIGSQ 475

Query: 482 DLLLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSLIFTCIVGVITTL 541
             LL+ ANTTGGV  K+ISPQSIAIA AAVG  GKES+LF+ TVK+S I   IV + T +
Sbjct: 476 AGLLIGANTTGGVMAKLISPQSIAIATAAVGETGKESELFQKTVKYSFILLGIVCIWTFI 535

Query: 542 QA 543
            A
Sbjct: 536 LA 537


Lambda     K      H
   0.328    0.140    0.436 

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: 814
Number of extensions: 32
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: 551
Length of database: 540
Length adjustment: 35
Effective length of query: 516
Effective length of database: 505
Effective search space:   260580
Effective search space used:   260580
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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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 2024 update 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