GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Pedobacter sp. GW460-11-11-14-LB5

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate CA265_RS15560 CA265_RS15560 glutamate/aspartate:proton symporter GltP

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__Pedo557:CA265_RS15560
          Length = 428

 Score =  448 bits (1153), Expect = e-130
 Identities = 221/405 (54%), Positives = 305/405 (75%), Gaps = 2/405 (0%)

Query: 5   LFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGM 64
           +F +L FQVL AI IGI +G ++P      K +  GF+ LI M+IAP+IF T+V GIA M
Sbjct: 10  VFSNLTFQVLLAIIIGIYVGAYFPGFAPTAKLISQGFINLISMLIAPIIFFTIVLGIAHM 69

Query: 65  ESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQA 124
             MK VGR G  ALLYFEIVST+A+ IGL++ NV++PGAGM       DA  +A YA+QA
Sbjct: 70  GDMKKVGRVGGKALLYFEIVSTVAIAIGLLVANVLKPGAGMIAKAG--DATKIAGYAEQA 127

Query: 125 KDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQV 184
           KD     F + +IP ++I +FA GNILQ+LLFA+LFG+ L++LG +G  + N  +  S+V
Sbjct: 128 KDMNWAEFFLHIIPHNIIASFAEGNILQILLFAILFGYGLNKLGGEGTTVLNAFDKISKV 187

Query: 185 IFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKA 244
           +F I+ +IMRLAPIGAFG MAF+IG +G+ ++V + +L+   Y+TC LF+ ++L  I + 
Sbjct: 188 LFKIMKLIMRLAPIGAFGGMAFSIGTHGLESIVGMAKLMGSVYLTCFLFIFVILNGICRY 247

Query: 245 TGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDG 304
             FS++ +++YIR+E+LIVLGTSSSESALP M+ KME +GC KSVVGLVIPTGYSFNLDG
Sbjct: 248 YNFSLWAYLKYIRQEILIVLGTSSSESALPSMMQKMEAIGCDKSVVGLVIPTGYSFNLDG 307

Query: 305 TSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 364
           T+IYL MA +F+ Q  +  + +  QIT+L VL+++SKGAAGVTGSGFIVL +TL+A+  +
Sbjct: 308 TAIYLAMAVIFLCQVFHVDLTLGQQITVLGVLMITSKGAAGVTGSGFIVLVSTLTALKIM 367

Query: 365 PVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKK 409
           P+  +++++G+DRFMSEARA+TN++GNGVATIV+AK  K+ D +K
Sbjct: 368 PIEHISILIGVDRFMSEARAITNVIGNGVATIVIAKSEKQFDEQK 412


Lambda     K      H
   0.327    0.142    0.401 

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: 558
Number of extensions: 23
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: 428
Length of database: 428
Length adjustment: 32
Effective length of query: 396
Effective length of database: 396
Effective search space:   156816
Effective search space used:   156816
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 (21.7 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