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

GapMind for catabolism of small carbon sources

Aligments 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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Steps (tab-delimited)
Rules (tab-delimited)
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, 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

GapMind for catabolism of small carbon sources