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

GapMind for catabolism of small carbon sources

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

Align Serine transporter (characterized)
to candidate 7026223 Shewana3_3365 serine transporter, putative (RefSeq)

Query= SwissProt::P0AAD6
         (429 letters)



>lcl|FitnessBrowser__ANA3:7026223 Shewana3_3365 serine transporter,
           putative (RefSeq)
          Length = 430

 Score =  473 bits (1218), Expect = e-138
 Identities = 238/429 (55%), Positives = 307/429 (71%), Gaps = 7/429 (1%)

Query: 1   METTQTSTIASKDSRSAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILA 60
           +ET Q ST  S      W + DT WML L+GTA+GAG+LFLPINAG+GG  PL++MAI+ 
Sbjct: 9   LETPQ-STQESTTRHLPWTRQDTTWMLSLFGTAVGAGILFLPINAGMGGFWPLVLMAIII 67

Query: 61  FPMTFFAHRGLTRFVLSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAI 120
            PMT+ AHRGL+RFV S   PG DIT+VVEEHFGIGAGK ITLLYF AIYPI+L+Y V I
Sbjct: 68  GPMTYLAHRGLSRFVCSSSIPGSDITQVVEEHFGIGAGKAITLLYFLAIYPIVLIYGVGI 127

Query: 121 TNTVESFMSHQLGMTPPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLA 180
           TNTV+SF+ +QLGM  PPR +LS +LI GMM ++  GEQ ++K   +LV+P VG+L  ++
Sbjct: 128 TNTVDSFIVNQLGMASPPRFLLSGVLIFGMMAVMVAGEQFMLKVTQLLVYPLVGILAFMS 187

Query: 181 LYLIPQWNGAALETLSLDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYG 240
           +YLIP+W   AL+ +  DT +  G     T+WL IPV+VF+FNHSP IS F+V+ + ++G
Sbjct: 188 IYLIPEWKMDALQVVP-DTGAFLG-----TVWLTIPVLVFAFNHSPAISQFSVSLKRDHG 241

Query: 241 DMAEQKCSKILAFAHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPV 300
             A +K   IL    +M+V  VM FVFSCVLSL+P  LA AK +N+ ILSYLAN  ++  
Sbjct: 242 VNAARKADVILRNTSMMLVGFVMLFVFSCVLSLSPEQLAEAKAKNLPILSYLANVHDSGF 301

Query: 301 IAWMAPIIAIIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTT 360
           +++  P IA +AI  SF GHY+GA EG  G+++K LR   K I  NKLN+   +FM  T 
Sbjct: 302 VSYFGPFIAFVAIVSSFFGHYMGATEGMKGIIVKQLRSSNKQISENKLNKFILVFMFATI 361

Query: 361 WIVATLNPSILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAI 420
           W VA  NPSILGMIE LGGPIIA IL+LMPMYA+ KVPA++ Y   ISNVFV++ GL+A+
Sbjct: 362 WAVAIKNPSILGMIEALGGPIIAAILYLMPMYAVYKVPALKAYRNRISNVFVIIAGLLAM 421

Query: 421 SAIFYSLFS 429
           +AI + L S
Sbjct: 422 TAILFGLLS 430


Lambda     K      H
   0.328    0.140    0.416 

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: 581
Number of extensions: 24
Number of successful extensions: 2
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: 429
Length of database: 430
Length adjustment: 32
Effective length of query: 397
Effective length of database: 398
Effective search space:   158006
Effective search space used:   158006
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 (21.8 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:

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