GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctP in Magnetospirillum magneticum AMB-1

Align L-lactate permease (characterized, see rationale)
to candidate WP_043745478.1 AMB_RS20875 L-lactate permease

Query= uniprot:Q8EIL2
         (545 letters)



>lcl|NCBI__GCF_000009985.1:WP_043745478.1 AMB_RS20875 L-lactate
           permease
          Length = 547

 Score =  734 bits (1894), Expect = 0.0
 Identities = 365/546 (66%), Positives = 446/546 (81%), Gaps = 11/546 (2%)

Query: 3   WTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVS 62
           W Q Y P G+LWL++++A +PI+FFF+AL +LKLKGH+AG +T+L+++AVAI+ YKMPV+
Sbjct: 4   WMQVYDPAGNLWLSSLIAAIPIIFFFVALAILKLKGHVAGTITVLLSIAVAIVFYKMPVA 63

Query: 63  IALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVGF 122
            A+ + + GF +GLWPIAWIII AVFLYK+TVKTGQFEIIRSSV+S+T DQRLQML++GF
Sbjct: 64  AAVMAGVQGFLFGLWPIAWIIIGAVFLYKVTVKTGQFEIIRSSVVSITADQRLQMLMIGF 123

Query: 123 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 182
           SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV
Sbjct: 124 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 183

Query: 183 SSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTSN 242
           S LD F IG +AGRQLP+L++ VPFW+I +MDG +G+R+TWPA LVAG SFA   + TSN
Sbjct: 184 SGLDAFKIGAMAGRQLPLLAVFVPFWIIFIMDGFKGVRETWPAILVAGGSFAFGVWFTSN 243

Query: 243 FIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQRAVTPKST--FSNGQIFKAWS 300
           +IGPELPDITSAL+SL+C+T+FLK WQPK IF F   K+     K +  ++ GQ+ +AW+
Sbjct: 244 YIGPELPDITSALISLVCITVFLKFWQPKNIFRF---KEEGEDEKHSHDYTTGQVARAWA 300

Query: 301 PFIILTAIVTLWSIKDVQL------ALSFATISIEVPYLHNLVIKTAPIVAKETPYAAIY 354
           PF+ILTA+VT+WS+K  +        L F  I+ EVP LHNLV K  PIVA      A+Y
Sbjct: 301 PFLILTAVVTVWSLKPFKAMFAKGGELVFTNINWEVPALHNLVAKVPPIVAAAKAVPAVY 360

Query: 355 KLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPILSIGLVLAFAFVANY 414
            LNL+ A GTAILI+A+I+I++L M  S  L +F +TL EL+ PI +IG VLAFA+VAN 
Sbjct: 361 TLNLVSATGTAILISAIITIIMLGMKGSEGLKTFGETLNELKRPIYTIGTVLAFAYVANA 420

Query: 415 SGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQIGVTPEL 474
           SGLS+TLAL+L G G  +PFFSP LGWLGVFLTGSDTSSNALFGALQA TA+Q+G++  L
Sbjct: 421 SGLSTTLALLLTGAGDFYPFFSPVLGWLGVFLTGSDTSSNALFGALQATTAHQLGISDIL 480

Query: 475 LVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGVLTVLQAY 534
           +VAANTTGGVTGKMISPQSIAVACAA GL G E++LFRFTLKHS+FF   IGV+T LQAY
Sbjct: 481 MVAANTTGGVTGKMISPQSIAVACAAVGLVGHEANLFRFTLKHSVFFVCIIGVITTLQAY 540

Query: 535 IVPWTL 540
           ++ W +
Sbjct: 541 VLTWMI 546


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: 1052
Number of extensions: 36
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: 547
Length adjustment: 35
Effective length of query: 510
Effective length of database: 512
Effective search space:   261120
Effective search space used:   261120
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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