Alignments for a candidate for lctP in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Pseudomonas stutzeri RCH2

Align L-lactate permease (characterized, see rationale)
to candidate GFF3767 Psest_3836 L-lactate permease

Query= uniprot:A0KZB2
         (547 letters)



>FitnessBrowser__psRCH2:GFF3767
          Length = 567

 Score =  462 bits (1189), Expect = e-134
 Identities = 248/553 (44%), Positives = 352/553 (63%), Gaps = 16/553 (2%)

Query: 2   TILQLLASLTPVISVMIFLVLLRMPASKAMPISMIITALAAVFIWQMDTTLLAASVLEGL 61
           T+L +LA   P++   + L+  R PA  AMP+  ++TAL  +  W M    + AS L+GL
Sbjct: 4   TLLSILA-FVPLVLAGVLLIGFRWPAKYAMPLVFVLTALIGLLAWDMTLNRVIASTLQGL 62

Query: 62  LSAITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSAG 121
           +     L IIFGA+ LLNTLK+SG + +IR GF+N+S D RVQV+I+ WLFG FIEG++G
Sbjct: 63  ILTAAILWIIFGAILLLNTLKHSGGISSIRRGFSNVSPDRRVQVLIVAWLFGCFIEGASG 122

Query: 122 FGTPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGMEQGLTQGGVSLAA 181
           FGTPAA+ APL+V LG P +AA V+ ++  S  VSFGA+G P+L G+  GL + G+S   
Sbjct: 123 FGTPAAVAAPLMVALGFPALAAVVMGMMVQSTPVSFGAVGTPILVGVGAGLDKTGIS--- 179

Query: 182 EQFAAHGGSYVGYARFIVMHMITIDLITGTLIPLVMVTILTGFFGRNKSFKEGLAIWKFA 241
           EQ AA G ++  +   I   +  I  + G L+PL+MV+I+T +FGRNKS+ EGLA+  FA
Sbjct: 180 EQLAAVGSNWEVFFHLIFSRVAIIHALCGILMPLIMVSIMTRYFGRNKSWTEGLAVAPFA 239

Query: 242 IFAGLAFTVPAWIINYLAGPEFPSVIGSLVGMALVIPVARKGYLLPKTPWNDFA---END 298
           +F GLAF +P        GPEFPS+IG+LVG+A+V+P A+ G+LLPK  W DFA   E  
Sbjct: 240 VFTGLAFVIPYAAAGVFLGPEFPSMIGALVGLAIVVPAAKAGFLLPKDTW-DFAPAKEWP 298

Query: 299 SQEGAKIETTAK-------FSQIAAWTPYIIMAALLVLSRTVAPLKAWLSSFNISWTGLM 351
           S+   KIE   +        S   AW PY+++A LLV SR     KA L S +  W  ++
Sbjct: 299 SEWMGKIEMKIEDVAGKTPISVPMAWAPYLLLAGLLVASRVFPDFKALLMSLSFGWKDIL 358

Query: 352 G-TELKASFATLYAPGAFFVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIISLGASVP 410
           G T +  +   LY PG     V ++ FFL +MK+  +  +I  S K++L     L  ++P
Sbjct: 359 GETGVSGTLEPLYLPGGILCMVVLITFFLHRMKASELGAAISESSKTLLGAGFVLIFTIP 418

Query: 411 MVKIFLNSGVNGAGLASMPVALADMLGQSMGAVWAWMAPIVGIFGAFLSGSATFSNMMFS 470
           MV+I +NSGVNG+ L SMPVA+A ++  S+G+V+ + AP VG  GAF++GS T SN+M S
Sbjct: 419 MVRILINSGVNGSDLVSMPVAMAQLVANSVGSVYPFFAPAVGALGAFIAGSNTVSNLMLS 478

Query: 471 SLQYSVADNIGMNHTLVLALQGIGANAGNMMCVMNVVAAATVVGMAGRESEIIRKTMPVA 530
             Q++ A  +G++  L++ALQ +GA AGNM+ + NVVAA+  VG+ GRE   +RKTM   
Sbjct: 479 QFQFNTAGLLGLSGALMVALQSVGAAAGNMIAIHNVVAASATVGLLGREGITLRKTMLPT 538

Query: 531 IGYALLAGTIATL 543
           + Y +LAG I  +
Sbjct: 539 LYYLILAGAIGLI 551


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: 965
Number of extensions: 57
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: 567
Length adjustment: 36
Effective length of query: 511
Effective length of database: 531
Effective search space:   271341
Effective search space used:   271341
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.

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
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