Alignments for a candidate for lctP in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Escherichia coli BW25113

Align L-lactate permease (characterized, see rationale)
to candidate 17664 b3603 L-lactate permease (NCBI)

Query= uniprot:Q8EIL2
         (545 letters)



>FitnessBrowser__Keio:17664
          Length = 551

 Score =  725 bits (1872), Expect = 0.0
 Identities = 368/547 (67%), Positives = 441/547 (80%), Gaps = 9/547 (1%)

Query: 3   WTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVS 62
           W Q Y P G++WL++++A LPI+FFF AL  LKLKG++A + T+ IALAVA++ YKMPV+
Sbjct: 4   WQQNYDPAGNIWLSSLIASLPILFFFFALIKLKLKGYVAASWTVAIALAVALLFYKMPVA 63

Query: 63  IALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVGF 122
            ALAS +YGF YGLWPIAWIII AVF+YKI+VKTGQF+IIRSS++S+T DQRLQML+VGF
Sbjct: 64  NALASVVYGFFYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITPDQRLQMLIVGF 123

Query: 123 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 182
            FGAFLEGAAGFGAPVAITAALLVGLGF PLYAAGLCLI NTAPVAFGAMGIPI+VAGQV
Sbjct: 124 CFGAFLEGAAGFGAPVAITAALLVGLGFKPLYAAGLCLIVNTAPVAFGAMGIPILVAGQV 183

Query: 183 SSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTSN 242
           + +D F IGQ+ GRQLP ++IIV FW++A+MDG RGI++TWPA +VAG SFA+ Q+L+SN
Sbjct: 184 TGIDSFEIGQMVGRQLPFMTIIVLFWIMAIMDGWRGIKETWPAVVVAGGSFAIAQYLSSN 243

Query: 243 FIGPELPDITSALVSLICLTLFLKVWQPKEIFTFS--GMKQRAVTPKST-FSNGQIFKAW 299
           FIGPELPDI S+LVSL+CLTLFLK WQP  +F F   G  Q  +T   T ++ GQ+ +AW
Sbjct: 244 FIGPELPDIISSLVSLLCLTLFLKRWQPVRVFRFGDLGASQVDMTLAHTGYTAGQVLRAW 303

Query: 300 SPFIILTAIVTLWSIKDVQL------ALSFATISIEVPYLHNLVIKTAPIVAKETPYAAI 353
           +PF+ LTA VTLWSI   +       AL    I+I VPYL  LV +  P+V++ T YAA+
Sbjct: 304 TPFLFLTATVTLWSIPPFKALFASGGALYEWVINIPVPYLDKLVARMPPVVSEATAYAAV 363

Query: 354 YKLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPILSIGLVLAFAFVAN 413
           +K +   A GTAIL AA++SIV LKM  S+A+++F  TL EL  PI SIG+VLAFAF++N
Sbjct: 364 FKFDWFSATGTAILFAALLSIVWLKMKPSDAISTFGSTLKELALPIYSIGMVLAFAFISN 423

Query: 414 YSGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIGVTPE 473
           YSGLSSTLAL LA TG AF FFSPFLGWLGVFLTGSDTSSNALF ALQA  A QIGV+  
Sbjct: 424 YSGLSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQIGVSDL 483

Query: 474 LLVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVLTVLQA 533
           LLVAANTTGGVTGKMISPQSIA+ACAA GL GKESDLFRFT+KHSL F   +GV+T LQA
Sbjct: 484 LLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSLIFTCIVGVITTLQA 543

Query: 534 YIVPWTL 540
           Y++ W +
Sbjct: 544 YVLTWMI 550


Lambda     K      H
   0.327    0.140    0.419 

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: 1052
Number of extensions: 44
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: 545
Length of database: 551
Length adjustment: 36
Effective length of query: 509
Effective length of database: 515
Effective search space:   262135
Effective search space used:   262135
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 17 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 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