GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctP in Klebsiella michiganensis M5al

Align L-lactate permease (characterized, see rationale)
to candidate BWI76_RS27185 BWI76_RS27185 L-lactate permease

Query= uniprot:Q8EIL2
         (545 letters)



>FitnessBrowser__Koxy:BWI76_RS27185
          Length = 551

 Score =  730 bits (1884), Expect = 0.0
 Identities = 366/547 (66%), Positives = 440/547 (80%), Gaps = 9/547 (1%)

Query: 3   WTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVS 62
           W Q Y P G++WL++++A LPI+FFF AL  LKLKG++A   T++IAL+VA++ YKMPV 
Sbjct: 4   WQQNYDPAGNIWLSSLIASLPILFFFFALIKLKLKGYVAATWTVVIALSVALLFYKMPVD 63

Query: 63  IALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVGF 122
            ALAS +YGF YGLWPIAWIII AVF+YKI+VKTGQF+IIRSS++S+T DQRLQML+VGF
Sbjct: 64  HALASVVYGFFYGLWPIAWIIIAAVFVYKISVKTGQFDIIRSSILSITPDQRLQMLIVGF 123

Query: 123 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 182
           SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLI NTAPVAFGAMGIPI+VAGQV
Sbjct: 124 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIVNTAPVAFGAMGIPILVAGQV 183

Query: 183 SSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTSN 242
           + LD F IGQ+ GRQLP L+IIV FW++A+MDG RGI++TWPA +VAG SFA+ Q+L+SN
Sbjct: 184 TGLDSFEIGQMVGRQLPFLTIIVLFWIMAIMDGWRGIKETWPAVMVAGGSFAIAQYLSSN 243

Query: 243 FIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQRAV---TPKSTFSNGQIFKAW 299
           F+GPELPDI S+LVSL+CLTLFLK WQP  IF F  M    V     ++ ++ GQ+ +AW
Sbjct: 244 FLGPELPDIISSLVSLVCLTLFLKRWQPVRIFRFGDMGASQVDMNLARTRYTPGQVIRAW 303

Query: 300 SPFIILTAIVTLWSIKDVQL------ALSFATISIEVPYLHNLVIKTAPIVAKETPYAAI 353
           SPF+ LTA VTLWS+   +       A+    I+I VP+L  +V +  P+V + TPYAA+
Sbjct: 304 SPFLFLTATVTLWSVPPFKALFAPGGAMYDFVINISVPFLDKMVARMPPVVNEATPYAAV 363

Query: 354 YKLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPILSIGLVLAFAFVAN 413
           YK + L A GTAIL AA++SIV L+M   +A+++F   L EL  PI SIG+VLAFAF++N
Sbjct: 364 YKFDWLSATGTAILFAALLSIVWLRMKPKDAISTFGSMLKELALPIYSIGMVLAFAFISN 423

Query: 414 YSGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIGVTPE 473
           YSGLSSTLAL LA TG AF FFSPFLGWLGVFLTGSDTSSNALF ALQA  A QIGV+  
Sbjct: 424 YSGLSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALFAALQATAAQQIGVSDI 483

Query: 474 LLVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVLTVLQA 533
           LLVAANTTGGVTGKMISPQSIA+ACAA GL GKESDLFRFT+KHSL F   +GV+T LQA
Sbjct: 484 LLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKHSLIFTCMVGVITTLQA 543

Query: 534 YIVPWTL 540
           Y++ W +
Sbjct: 544 YVLTWMI 550


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: 1051
Number of extensions: 42
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: 551
Length adjustment: 36
Effective length of query: 509
Effective length of database: 515
Effective search space:   262135
Effective search space used:   262135
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