GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctP in Paraburkholderia bryophila 376MFSha3.1

Align L-lactate permease (characterized, see rationale)
to candidate H281DRAFT_00392 H281DRAFT_00392 lactate permease

Query= uniprot:Q8EIL2
         (545 letters)



>FitnessBrowser__Burk376:H281DRAFT_00392
          Length = 532

 Score =  397 bits (1020), Expect = e-115
 Identities = 220/534 (41%), Positives = 321/534 (60%), Gaps = 13/534 (2%)

Query: 5   QTYTPLG-SLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVSI 63
           Q  TP+G SL  + +VA LPI+   L L   +     A    L++ L VAI  ++ PV +
Sbjct: 4   QLLTPVGNSLLPSFLVAALPIIVVLLLLGWARRPAWQASLAGLIVGLVVAIAVWQFPVRL 63

Query: 64  ALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVI-SVTEDQRLQMLLVGF 122
           AL S   G  +  WP+ WI+ TA+ LY I  ++G+F   R  +I ++  D+R+ +++VGF
Sbjct: 64  ALDSVAAGVVFACWPVMWIVFTAILLYNIAQRSGRFAAFRMWMIDNLPNDRRVVLVVVGF 123

Query: 123 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 182
           SFGA LEG +GFG PVAIT++LL+ LGF  L A    LI NTAPVAFGA+G+PI V G V
Sbjct: 124 SFGALLEGISGFGTPVAITSSLLILLGFPTLEALTFTLIFNTAPVAFGALGVPITVLGAV 183

Query: 183 SSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTSN 242
           + L    + ++ GRQLP  ++++PF++IA+  G R + + WP  LV+G SFA+TQF+ SN
Sbjct: 184 THLPADSLAKMVGRQLPFFALLLPFYVIAVYAGFRNMVRVWPVLLVSGASFALTQFVASN 243

Query: 243 FIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQRAVTPKSTFSNGQIFKAWSPF 302
           ++   L D+ S++VSL+    FL+VW+P     F+    R    +      Q    W P+
Sbjct: 244 YVNYSLTDVLSSMVSLVVTIAFLRVWKPAVDPAFAVNIDRVGEVRGKIGGSQ---GWYPW 300

Query: 303 IILTAIVTLWSIKDVQLALSFATISIEVPYLHNLVIKTAPIVAKETPYAAIYKLNLLGAV 362
           II++ +V +W++  + L      + +  P L   V     I    TPY AI+    L A 
Sbjct: 301 IIVSVVVIVWTVAKIFL---IGDVKVPWPGLDKAVF----ITLYNTPYGAIWDFQPL-AT 352

Query: 363 GTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPILSIGLVLAFAFVANYSGLSSTLA 422
           GTAIL+AA+I+ +V+ +S  +   +  DT ++ R  IL++  ++  A++ NYSGL+ TL 
Sbjct: 353 GTAILVAAIITSLVVGLSARDFGAAIVDTWVQTRIAILTVATIVGLAYLMNYSGLTYTLG 412

Query: 423 LVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIGVTPELLVAANTTG 482
           L +A  G  FP  S FLGW+ VFL+GSDTS NALFG LQ   ANQ+ + P L+ A N++G
Sbjct: 413 LGVASVGPFFPLVSAFLGWVAVFLSGSDTSGNALFGNLQVVAANQLNLNPVLMAATNSSG 472

Query: 483 GVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVLTVLQAYIV 536
           GV GKMISPQ+I+   A T L GKE  +F  T KHS+     +G+L  LQ  ++
Sbjct: 473 GVMGKMISPQNISTGVATTDLKGKEGVVFAKTFKHSILLTVLLGILVWLQQNVL 526


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: 882
Number of extensions: 36
Number of successful extensions: 6
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: 532
Length adjustment: 35
Effective length of query: 510
Effective length of database: 497
Effective search space:   253470
Effective search space used:   253470
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: 52 (24.6 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