Alignments for a candidate for lctP in Brevibacterium jeotgali SJ5-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Brevibacterium jeotgali SJ5-8

Align L-lactate permease (characterized, see rationale)
to candidate WP_101588112.1 BJEO58_RS04570 L-lactate permease

Query= uniprot:L0GFN1
         (564 letters)



>NCBI__GCF_900169175.1:WP_101588112.1
          Length = 618

 Score =  527 bits (1358), Expect = e-154
 Identities = 280/560 (50%), Positives = 379/560 (67%), Gaps = 14/560 (2%)

Query: 7   ALFAFTPILLAAIMLIGLRWPASRAMPLVFLFTAAIGLFVWDMSVNRIIASTLQGLVITL 66
           AL A +PIL+A I+L+  R PA+ AMP   +  A +  F W +S   I AS +QG+++ L
Sbjct: 8   ALLAASPILVAGILLLVFRAPATVAMPAALVVAALVAFFGWGISAVTISASVIQGIIVAL 67

Query: 67  GLLWIIFGAILLLNTLKHSGGITAIRAGFTTISPDRRIQAIIIAWLFGCFIEGASGFGTP 126
           GLLWI+FGA+LLL+TL  SG I +I+AGF +ISPDRRIQ IIIAWLFG FIEGA+GFG P
Sbjct: 68  GLLWIVFGALLLLSTLTKSGAIDSIKAGFVSISPDRRIQVIIIAWLFGSFIEGAAGFGAP 127

Query: 127 AAIAAPLLVAVGFPAMAAVLLGMLVQSTPVSFGAVGTPIVVGINSGLDTATIGA------ 180
           AA+ APLL+A+GFPA+AAVL G+L+QSTPVSFGAVGTP++ GI  GL +   G       
Sbjct: 128 AAVVAPLLLALGFPAVAAVLAGLLIQSTPVSFGAVGTPMLTGIGQGLLSGDSGRFPQPIL 187

Query: 181 -QLVAQG-SSWNAYLQQITSSVAITHAIVGTVMPLVMVLMLTRFFGKEKSWKAGFEVLPF 238
            ++   G +  +A++    + VA  HAI G ++P+++V  +TRFFG++KS++AG  V PF
Sbjct: 188 DRMAELGITEQSAFVAHTAAQVATIHAICGLMIPIILVCFMTRFFGEQKSFRAGLAVAPF 247

Query: 239 AIFAGLAFTLPYAATGIFLGPEFPSLLGGLVGLAIVTTAARFKFLTPKTTWDFADAKEWP 298
           A FA  +F +PY      LGPEFP+LLGG++GL IV +AAR  FL PK TW+FA    WP
Sbjct: 248 AFFAAASFVVPYVLVAYLLGPEFPALLGGIIGLLIVVSAARAGFLQPKDTWEFAPRHRWP 307

Query: 299 AEWLGTIEMKLDE-MAARPMSAFRAWLPYVLVGAILVISRVFPQVTAALKS-VSIAFANI 356
             W+G ++ + +E +  + M    AW PY+++ A+L+++R  P +   L   V+I F N+
Sbjct: 308 DRWMGNVDPRDEEVILEKKMPLVLAWSPYLIIVALLLLTRNIPPLKEFLSGPVAIDFTNL 367

Query: 357 LGETGINAGIEPLYLPGGILVMVVLITFFLHGMRVSELKAAVKESSGVLLSAGFVLLFTV 416
           LG T I+   + LY PG + ++  L+T  L  M  S++  A K +   +  A F LL +V
Sbjct: 368 LG-TSISQTSDLLYSPGFLFIIAALLTIPLQRMTRSQVAGAWKIAGRQIAGAAFALLCSV 426

Query: 417 PMVRILINSG--VNGAELASMPIVMARYVADSVGSIYPLLAPAVGALGAFLAGSNTVSNM 474
           PMVR+ INSG   N   + SMP+ +A   A S+GS +PL+AP VGALGAF+AGSNTVSN+
Sbjct: 427 PMVRVFINSGSDFNSTGMESMPLTLAEAAASSLGSAWPLVAPFVGALGAFVAGSNTVSNL 486

Query: 475 MFSQFQFGVAQSLGI-SGAMVVATQAVGAAAGNMVAIHNVVAASATVGLLGREGSTLRKT 533
           MFSQFQ+    +LG+ S   VVA QAVG AAGNMV++HNVVAA+ATVGLLGREG  LRKT
Sbjct: 487 MFSQFQYATGANLGVGSPETVVAAQAVGGAAGNMVSVHNVVAAAATVGLLGREGEILRKT 546

Query: 534 IWPTLYYVLFTGVIGLIAIY 553
             P + Y L  G I  + ++
Sbjct: 547 ALPMVVYSLMAGSIAFMMVF 566


Lambda     K      H
   0.326    0.140    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: 1015
Number of extensions: 53
Number of successful extensions: 7
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: 564
Length of database: 618
Length adjustment: 37
Effective length of query: 527
Effective length of database: 581
Effective search space:   306187
Effective search space used:   306187
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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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