GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__azobra:AZOBR_RS25125 AZOBR_RS25125 L-lactate
           permease
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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