Aligments for a candidate for alsT in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Aligments for a candidate for alsT in Shewanella sp. ANA-3

Align Sodium/proton-dependent alanine carrier protein (characterized)
to candidate 7024292 Shewana3_1484 amino acid carrier protein (RefSeq)

Query= SwissProt::P30145
         (445 letters)



>lcl|FitnessBrowser__ANA3:7024292 Shewana3_1484 amino acid carrier
           protein (RefSeq)
          Length = 494

 Score =  463 bits (1191), Expect = e-135
 Identities = 236/431 (54%), Positives = 300/431 (69%), 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 +  +L+PG+QAN
Sbjct: 103 SSAFVESTLGQVYKEKINGEYRGGPAFYIEKGLGMKWYAWTFAIATIFACGILLPGVQAN 162

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

Query: 180 ANIEKVPDVFGLIFKSAFGADQVFGGILGSAVMWGVKRGLYANEAGQGTGAHPAAAAEVS 239
            NI ++PD+  LI KSAFG D  FG ILG A+MWGVKRG+Y+NEAGQGTG H ++AA VS
Sbjct: 223 LNIGQLPDIIMLILKSAFGLDAGFGAILGLAIMWGVKRGIYSNEAGQGTGPHASSAAAVS 282

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

Query: 300 AAVDTLFPGFGSAFIAIALFFFAFTTMYAYYYIAETNLAYLVRSEKRGTAFFALKLVFLA 359
            A++++ PGFG+ F+A+ALFFFAFTT+ AYYYIAETN+AY+ R   R      LK+V +A
Sbjct: 342 TAMESMMPGFGNMFVAVALFFFAFTTIVAYYYIAETNIAYINRKANRPWLTVVLKVVLMA 401

Query: 360 ATFYGTVKTATTAWAMGDIGLGIMVWLNLIAILLLFKPAYMALKDYEEQLKQGKDPEFNA 419
           +T YGTVKTA  AW MGDIG+G+M WLN+IAI+LL + A+  LKDYE Q KQG +P F+ 
Sbjct: 402 STVYGTVKTADLAWGMGDIGVGLMAWLNIIAIILLQRIAFTCLKDYESQQKQGVEPLFDP 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: 673
Number of extensions: 32
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: 494
Length adjustment: 33
Effective length of query: 412
Effective length of database: 461
Effective search space:   189932
Effective search space used:   189932
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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Protein sequences (fasta format)
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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