GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltP in Shewanella loihica PV-4

Align Na+/H+ dicarboxylate symporter (characterized, see rationale)
to candidate 5208231 Shew_0743 sodium:dicarboxylate symporter (RefSeq)

Query= uniprot:L0GT47
         (419 letters)



>lcl|FitnessBrowser__PV4:5208231 Shew_0743 sodium:dicarboxylate
           symporter (RefSeq)
          Length = 433

 Score =  476 bits (1225), Expect = e-139
 Identities = 233/404 (57%), Positives = 315/404 (77%), Gaps = 1/404 (0%)

Query: 17  LPLWQQILIGLALGVAAGMAFGADAQLLAPIGTLFLNAIKMLIVPLVFVSLVAGITSMQD 76
           +PLW QILIG+ LG+ AG+  G  A LL PIGTLF+N IKMLIVPLVF SL+ G+TSMQD
Sbjct: 20  VPLWLQILIGMLLGICAGLGLGEQAVLLKPIGTLFVNTIKMLIVPLVFCSLIVGVTSMQD 79

Query: 77  SAKLGRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNMVASGNEQA-KQAPSLVSIL 135
           +AK+GRI  K+ A YL TT+ A+++GL  G +  PG G+ M ++ +  A K+ PS++  L
Sbjct: 80  TAKMGRIGFKSFAFYLGTTSIAITLGLAVGHIMQPGAGLAMTSAESHNAVKEVPSIMETL 139

Query: 136 VGLVPANPVTAFAEGNILQIIVFAIALGVSINLIGERGAPAVRLFDALAETFYKLTDLVM 195
           + +VP NP+ A A G ILQ+IVFA+ALG+++ LIG+ G PA+++F++LAE  YKLTD+VM
Sbjct: 140 INIVPTNPIAALASGQILQVIVFAVALGIALVLIGDHGKPAIKVFESLAEAMYKLTDMVM 199

Query: 196 RVAPIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGLLGLLARLNPLRF 255
           ++AP GVF L A V G +G ++L+PL  VI  +Y+    H++  Y  +L  +A+LNP++F
Sbjct: 200 KLAPYGVFGLMAWVAGEYGMDMLMPLIKVILAVYIGCALHIIGFYSLVLTFVAKLNPMQF 259

Query: 256 FQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGTAIYQGV 315
           F+GI+ ALAVA++TSSS+GTLP S++CA ++LG+++ ++ FVLP+G TINMDGTA+YQGV
Sbjct: 260 FKGISNALAVAYTTSSSAGTLPASMKCASESLGINKKISSFVLPLGTTINMDGTALYQGV 319

Query: 316 LALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAGLPLEGVALI 375
            ALF+AQAFGIDL+   Y  IILTATLASIGTAG+PGAGL+ML LVLT  GLPLEGVA+I
Sbjct: 320 TALFVAQAFGIDLTWVDYITIILTATLASIGTAGVPGAGLVMLTLVLTTVGLPLEGVAII 379

Query: 376 AGIDRILDMARTTVNVAGDLMTTTLVGRSEQELDRAIYDSSNKE 419
           AGIDRILDMART VNV+GDL+ TT++ +SE ELD   Y++  ++
Sbjct: 380 AGIDRILDMARTVVNVSGDLVATTVIAKSEDELDLEHYNADAEQ 423


Lambda     K      H
   0.324    0.140    0.386 

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: 649
Number of extensions: 31
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: 419
Length of database: 433
Length adjustment: 32
Effective length of query: 387
Effective length of database: 401
Effective search space:   155187
Effective search space used:   155187
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: 41 (22.0 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 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