GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alsT in Shewanella oneidensis MR-1

Align Sodium/proton-dependent alanine carrier protein (characterized)
to candidate 202182 SO3063 sodium:alanine symporter family protein (NCBI ptt file)

Query= SwissProt::P30145
         (445 letters)



>FitnessBrowser__MR1:202182
          Length = 495

 Score =  465 bits (1196), Expect = e-135
 Identities = 237/431 (54%), Positives = 303/431 (70%), Gaps = 2/431 (0%)

Query: 1   MIRLVTMGKSSEAGVSSFQALTMSLSGRIGVGNVAGTATGIAYGGPGAVFWMWVITFIGA 60
           MIRL+  GKS++AGVSSFQAL M+L+GR+G GN+AG AT I +GGPGA+FWMW++ F+GA
Sbjct: 43  MIRLMFDGKSTDAGVSSFQALAMTLAGRVGTGNIAGVATAITFGGPGALFWMWMVAFLGA 102

Query: 61  ATAYVESTWRKFIKRNKTDNTVAVRRSTLKKALAGNGLRCSRA-AIILSMAVLMPGIQAN 119
           ++A+VEST  +  K              ++K L       + A A I +  VL+PG+QAN
Sbjct: 103 SSAFVESTLGQVYKEKINGEYRGGPAFYIEKGLGMKWYAWTFAIATIFACGVLLPGVQAN 162

Query: 120 SIADSFSNAFGIPKLVTGIFVIAVLGFTIFGGVKRIAKTAEIVVPFMAVGYLFVAIAIIA 179
           SI  S   AF I   VT   +  +LGF IFGGVKRIA  A +VVPFMA+GY+ VA  IIA
Sbjct: 163 SIGASLKTAFDIDPNVTAAVLAMLLGFIIFGGVKRIANFATLVVPFMALGYIIVACVIIA 222

Query: 180 ANIEKVPDVFGLIFKSAFGADQVFGGILGSAVMWGVKRGLYANEAGQGTGAHPAAAAEVS 239
            NI+++P +  LI KSAFG D  FG ILG A+MWGVKRG+Y+NEAGQGTG H ++AA V+
Sbjct: 223 LNIDQLPGILWLIIKSAFGFDAGFGAILGLAIMWGVKRGVYSNEAGQGTGPHASSAAAVT 282

Query: 240 HPAKQGLVQAFSIYLDVFLVVTATALMILFTGQYNVINEKTGETIVEHLKGVEPGAGYTQ 299
           HPAKQGLVQAFS+Y+D   V +AT  M+L TG YNV     G  +   + GV  G+GY Q
Sbjct: 283 HPAKQGLVQAFSVYIDTLFVCSATGFMLLITGLYNV-QGPDGAALYTGIAGVAAGSGYVQ 341

Query: 300 AAVDTLFPGFGSAFIAIALFFFAFTTMYAYYYIAETNLAYLVRSEKRGTAFFALKLVFLA 359
            A++++ PGFG+ F+AIALFFFAFTT+ AYYYIAETN+AY+ R   R      LK++ +A
Sbjct: 342 TAMESMMPGFGNMFVAIALFFFAFTTIVAYYYIAETNIAYINRKVNRPWLTVMLKVIIMA 401

Query: 360 ATFYGTVKTATTAWAMGDIGLGIMVWLNLIAILLLFKPAYMALKDYEEQLKQGKDPEFNA 419
           +T YGTVKTA  AW MGDIG+GIM WLN+IAI+LL K A+  LKDYE Q KQG +P+F+ 
Sbjct: 402 STVYGTVKTADLAWGMGDIGVGIMAWLNIIAIILLQKVAFTCLKDYESQQKQGIEPQFDP 461

Query: 420 SKYGIKNAKFW 430
            K GI +A +W
Sbjct: 462 EKLGIPHADYW 472


Lambda     K      H
   0.324    0.137    0.407 

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: 685
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: 445
Length of database: 495
Length adjustment: 33
Effective length of query: 412
Effective length of database: 462
Effective search space:   190344
Effective search space used:   190344
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 51 (24.3 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