Alignments for a candidate for leuT in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for leuT in Shewanella loihica PV-4

Align The amino acid (leucine):2 Na+ symporter, LeuTAa (Yamashita et al., 2005). LeuT possesses two ion binding sites, NA1 and NA2, both highly specific for Na+ but with differing mechanisms of binding (Noskov and Roux, 2008). X-ray structures have been determined for LeuT in substrate-free outward-open and apo inward-open states (characterized)
to candidate 5210455 Shew_2896 sodium:neurotransmitter symporter (RefSeq)

Query= TCDB::O67854
         (513 letters)



>FitnessBrowser__PV4:5210455
          Length = 503

 Score =  217 bits (553), Expect = 7e-61
 Identities = 152/479 (31%), Positives = 237/479 (49%), Gaps = 49/479 (10%)

Query: 3   VKREHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIE 62
           +KRE W +R+G ILA  G+A+GLGN  RFP  A +NGGGAF IPY+ A +  GIP M +E
Sbjct: 1   MKREQWNSRVGFILAAVGSAIGLGNIWRFPYMAYDNGGGAFFIPYLFAMITAGIPFMIME 60

Query: 63  WAMGRYGGAQGHGTTPAIFYLLWRNRFAKI--LGVFGLWIPLVVAIYYVYIESWTLGFAI 120
           +++G     +   T+P IF  L      ++  LG F ++I  V+A+YYV I  WTL + +
Sbjct: 61  FSLGH----KIKKTSPRIFAQLGHTLGFRLEWLGWFQVFIAAVIAVYYVAIIGWTLSY-L 115

Query: 121 KFLVGLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEP--ILKPSLFAYIVFLITMFI 178
            F         PN            +F +++      + P  + +  +   I   I   +
Sbjct: 116 GFSFSQAWGDNPN------------DFFFNHYLKLGNNSPSHLGEFQIGIAIAMSIAWLM 163

Query: 179 NVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKL 238
               +  G+  GIER  KI MP LFI+ + L+ R+  L      A  GLN+L+ PDF +L
Sbjct: 164 TFMAVFTGVKGGIERANKIMMPMLFIMVLVLIGRIMFLPG----ALSGLNYLFEPDFSRL 219

Query: 239 KDPGVWIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSIS 298
            D  VW AA GQIFFTLS+GF  ++ Y+SY+    DI          N    V++    S
Sbjct: 220 LDAQVWSAAYGQIFFTLSVGFAIMLAYSSYLPTKADI--------NNNAFMTVLINCGFS 271

Query: 299 IPAAVAFFGVANAVAIAK--------AGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFF 350
           I A +  FGV   +A  +        +    L F+T+P   +       LG L+F  L  
Sbjct: 272 ILAGILIFGVLGYMAEEQMKPLTEVVSSGIGLAFVTIPTAINLMPAPYILGPLFFIALVI 331

Query: 351 AGLTSSIAIMQPMIAFLEDELKLSRKHAVLWTAAIVF-----FSAHLVMFLNKSLDEMDF 405
           AGL+S I+I++ + + + D+  + RK A +   ++ +     F+ +  + L   LD +D+
Sbjct: 332 AGLSSHISIIEAVTSAVIDKFHVRRKPAAVLVCSLGYLVSMAFATNGGLLL---LDLVDY 388

Query: 406 WAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLL 464
           +   I ++   L EL+I  W+       +  N     +V   +   +R+I+PA LA +L
Sbjct: 389 FINNIALLLSCLLELVIITWLLKVTVIHQHANENSEFRVGGWFVVCLRFISPAILATIL 447


Lambda     K      H
   0.330    0.146    0.463 

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: 703
Number of extensions: 43
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 513
Length of database: 503
Length adjustment: 34
Effective length of query: 479
Effective length of database: 469
Effective search space:   224651
Effective search space used:   224651
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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:

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
the source code
instructions for running GapMind on your computer

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