Alignments for a candidate for lctP in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Azospirillum brasilense Sp245

Align L-lactate permease (characterized, see rationale)
to candidate AZOBR_RS25125 AZOBR_RS25125 L-lactate permease

Query= uniprot:Q8EIL2
         (545 letters)



>FitnessBrowser__azobra:AZOBR_RS25125
          Length = 562

 Score =  764 bits (1972), Expect = 0.0
 Identities = 384/558 (68%), Positives = 459/558 (82%), Gaps = 20/558 (3%)

Query: 3   WTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVS 62
           WTQ Y P G+LWL+A+VA LPI+FFF+ALT+L++KGH+AG +T+ I+LAVAI+ YKMPV 
Sbjct: 4   WTQVYDPAGNLWLSALVAALPIIFFFIALTMLRMKGHVAGTITVAISLAVAILFYKMPVG 63

Query: 63  IALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVGF 122
           +ALASA YGF YGLWPIAWII+ AVFLYKITVKTGQFEIIRSSV+S+TEDQRLQML+VGF
Sbjct: 64  MALASAGYGFLYGLWPIAWIIVAAVFLYKITVKTGQFEIIRSSVVSITEDQRLQMLMVGF 123

Query: 123 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 182
           SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV
Sbjct: 124 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 183

Query: 183 SSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTSN 242
           +SLDPF IG +AGRQLP+LS+ VPFW+I +MDG +G+R+TWPA LVAG +FAVTQ+ T+N
Sbjct: 184 TSLDPFRIGAMAGRQLPLLSVFVPFWIIMIMDGWKGVRETWPAILVAGGTFAVTQYFTAN 243

Query: 243 FIGPELPDITSALVSLICLTLFLKVWQPKEIFTFS--------------GMKQRAVTPKS 288
           FIGPELPDITSALVSL+ +T+FLK W+PK IF F+               M       + 
Sbjct: 244 FIGPELPDITSALVSLVSITVFLKFWKPKAIFRFANSPLASGPVPQSVGAMASSEFNAQR 303

Query: 289 TFSNGQIFKAWSPFIILTAIVTLWSIKDVQL------ALSFATISIEVPYLHNLVIKTAP 342
           ++S G+I KAWSPF+ILT IVT+WS+K  +       AL+   +   +  L  LV+K AP
Sbjct: 304 SYSAGEIAKAWSPFLILTVIVTIWSLKPFKALFVKGGALADTVLYFPIAGLDKLVLKAAP 363

Query: 343 IVAKETPYAAIYKLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPILSI 402
           IVA   P  A+YKL+LL A GTAILI+A+I++V+LKM  ++ + +F +T+ EL+ PI SI
Sbjct: 364 IVASPKPIDAVYKLDLLAATGTAILISAIITMVMLKMRPADGVKTFVETVSELKRPIYSI 423

Query: 403 GLVLAFAFVANYSGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQA 462
           G+VLAFAF+ANYSGLSSTLAL+LAGTG  FPFFSP LGWLGVFLTGSDTSSNALF  LQA
Sbjct: 424 GMVLAFAFIANYSGLSSTLALLLAGTGFLFPFFSPILGWLGVFLTGSDTSSNALFCGLQA 483

Query: 463 NTANQIGVTPELLVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFC 522
            TA Q+GV+  L+VAANTTGGVTGKMISPQSIAVACAA GL G+ES+LFRFT+KHSLFF 
Sbjct: 484 TTAQQVGVSDVLMVAANTTGGVTGKMISPQSIAVACAAVGLVGRESELFRFTVKHSLFFV 543

Query: 523 TFIGVLTVLQAYIVPWTL 540
             IGV+T++QAYI+PW +
Sbjct: 544 AIIGVITMIQAYILPWMI 561


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: 1086
Number of extensions: 31
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: 562
Length adjustment: 36
Effective length of query: 509
Effective length of database: 526
Effective search space:   267734
Effective search space used:   267734
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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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