GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctP in Azospirillum brasilense Sp245

Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate AZOBR_RS25125 AZOBR_RS25125 L-lactate permease

Query= reanno::pseudo5_N2C3_1:AO356_07550
         (564 letters)



>FitnessBrowser__azobra:AZOBR_RS25125
          Length = 562

 Score =  787 bits (2032), Expect = 0.0
 Identities = 394/565 (69%), Positives = 468/565 (82%), Gaps = 7/565 (1%)

Query: 1   MQTWQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNM 60
           MQ W Q+Y P G+L LSAL A +PI+FFF+AL + R+KGHVAG+IT+A+++AVAI  + M
Sbjct: 1   MQPWTQVYDPAGNLWLSALVAALPIIFFFIALTMLRMKGHVAGTITVAISLAVAILFYKM 60

Query: 61  PADMAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLL 120
           P  MA A+AGYGF YGLWPIAWIIVAAVFLYK+TVK+GQFE+IRSSV+SIT+DQRLQ+L+
Sbjct: 61  PVGMALASAGYGFLYGLWPIAWIIVAAVFLYKITVKTGQFEIIRSSVVSITEDQRLQMLM 120

Query: 121 IGFCFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVA 180
           +GF FGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGA+GIPIIVA
Sbjct: 121 VGFSFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVA 180

Query: 181 GQVTGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYF 240
           GQVT +D F+IGAM GRQLPLLS+FVPFW++ +MDG +GVRETWPA LVAG +FA+TQYF
Sbjct: 181 GQVTSLDPFRIGAMAGRQLPLLSVFVPFWIIMIMDGWKGVRETWPAILVAGGTFAVTQYF 240

Query: 241 TSNFIGPELPDITSALASLISLTLFLKVWQPK---RTAGAQIAGATSSATVTASVGGFGQ 297
           T+NFIGPELPDITSAL SL+S+T+FLK W+PK   R A + +A    S  V  SVG    
Sbjct: 241 TANFIGPELPDITSALVSLVSITVFLKFWKPKAIFRFANSPLA----SGPVPQSVGAMAS 296

Query: 298 PRSTVASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYGWVFNFAIPHLDQ 357
                   YS GEI KAWSPFLILTV+VTIW+LKPFKA+F  GG++   V  F I  LD+
Sbjct: 297 SEFNAQRSYSAGEIAKAWSPFLILTVIVTIWSLKPFKALFVKGGALADTVLYFPIAGLDK 356

Query: 358 MVIKVAPIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKETLFEL 417
           +V+K APIV +P  I AV+KLD ++ATGTAI  SA+I+M++LK+    G+ TF ET+ EL
Sbjct: 357 LVLKAAPIVASPKPIDAVYKLDLLAATGTAILISAIITMVMLKMRPADGVKTFVETVSEL 416

Query: 418 RWPILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNA 477
           + PI SIGMVLAFAF+ NYSG+SST+AL+LAGTG  FPFFSP LGWLGVFLTGSDTSSNA
Sbjct: 417 KRPIYSIGMVLAFAFIANYSGLSSTLALLLAGTGFLFPFFSPILGWLGVFLTGSDTSSNA 476

Query: 478 LFSSLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTL 537
           LF  LQATTA Q+GV+D L+VAANT+GGVTGKMISPQSIAVACAA GLVG+ES+LFRFT+
Sbjct: 477 LFCGLQATTAQQVGVSDVLMVAANTTGGVTGKMISPQSIAVACAAVGLVGRESELFRFTV 536

Query: 538 KHSLFFATIVGLITLAQAYWFTGML 562
           KHSLFF  I+G+IT+ QAY    M+
Sbjct: 537 KHSLFFVAIIGVITMIQAYILPWMI 561


Lambda     K      H
   0.327    0.139    0.422 

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: 948
Number of extensions: 34
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: 564
Length of database: 562
Length adjustment: 36
Effective length of query: 528
Effective length of database: 526
Effective search space:   277728
Effective search space used:   277728
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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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:

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:

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:

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:

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