GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Herbaspirillum seropedicae SmR1

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate HSERO_RS13105 HSERO_RS13105 C4-dicarboxylate ABC transporter

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__HerbieS:HSERO_RS13105
          Length = 441

 Score =  591 bits (1524), Expect = e-173
 Identities = 296/415 (71%), Positives = 350/415 (84%)

Query: 2   KTSLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGI 61
           K  L+KSLYFQVL AI IGILLGHFYP  GE MKPLGDGFVKLIKMIIAPVIFCTVV GI
Sbjct: 5   KPPLYKSLYFQVLVAIVIGILLGHFYPSTGEAMKPLGDGFVKLIKMIIAPVIFCTVVIGI 64

Query: 62  AGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYA 121
           AGME MK VG+TG +ALLYFE+VST+ALIIGL++VN +QPG GMNVDPA+LD K++A Y 
Sbjct: 65  AGMEDMKKVGKTGGLALLYFEVVSTVALIIGLLLVNFLQPGVGMNVDPASLDTKSIAAYT 124

Query: 122 DQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESF 181
              K   +  F++ +IP S++ AFA G++LQVLL AVLFGFALH+ G +G L+F+ IE  
Sbjct: 125 APGKMGSVTDFVLGIIPTSMVDAFAKGDVLQVLLVAVLFGFALHKFGGRGTLVFDFIEKI 184

Query: 182 SQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSI 241
           S V+F ++  IM++APIGAFGAM+FTIGKYGVG+L  L +L+  FY+TC+LF+ +VLG I
Sbjct: 185 SHVLFSVVGAIMKVAPIGAFGAMSFTIGKYGVGSLFSLAKLMGTFYLTCLLFIFVVLGII 244

Query: 242 AKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFN 301
            +  GFSI+KF++YI+EELLIVLGTSSSES LPRML KME  G +K+VVGLVIPTGYSFN
Sbjct: 245 TRLHGFSIWKFVKYIKEELLIVLGTSSSESVLPRMLAKMENAGAKKTVVGLVIPTGYSFN 304

Query: 302 LDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAV 361
           LDGT+IYLTMAAVFIAQATN+ M  V ++TLL VLLL+SKGAAG+TGSGFIVLAATLSAV
Sbjct: 305 LDGTAIYLTMAAVFIAQATNTPMTFVQELTLLGVLLLTSKGAAGITGSGFIVLAATLSAV 364

Query: 362 GHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNN 416
           GH+PVAGLALILGIDRFMSEARALTN +GNGVAT+VVAKW  ELD ++L  VLNN
Sbjct: 365 GHVPVAGLALILGIDRFMSEARALTNTIGNGVATLVVAKWSGELDSERLTKVLNN 419


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: 650
Number of extensions: 28
Number of successful extensions: 1
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: 441
Length adjustment: 32
Effective length of query: 396
Effective length of database: 409
Effective search space:   161964
Effective search space used:   161964
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