GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Herbaspirillum seropedicae SmR1

Align CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate HSERO_RS05190 HSERO_RS05190 sugar ABC transporter substrate-binding protein

Query= TCDB::P25548
         (354 letters)



>FitnessBrowser__HerbieS:HSERO_RS05190
          Length = 357

 Score =  543 bits (1400), Expect = e-159
 Identities = 275/355 (77%), Positives = 310/355 (87%), Gaps = 1/355 (0%)

Query: 1   MKSIISLMA-ACAIGAASFAAPAFAQDKGSVGIAMPTKSSARWIDDGNNIVKQLQEAGYK 59
           +KS++S +A    +   S +A   AQ K  VG+AMPTKSSARWI DGNN+VK L+E GY+
Sbjct: 3   IKSVLSGIALGLGVTLMSISAQVSAQSKQLVGVAMPTKSSARWIADGNNMVKVLKEKGYQ 62

Query: 60  TDLQYADDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIR 119
           TDLQYA+DDIPNQLSQIENM+TKG KVLVIA+IDGTTL+DVL++A ++G+KVIAYDRLIR
Sbjct: 63  TDLQYAEDDIPNQLSQIENMLTKGAKVLVIAAIDGTTLTDVLQKAADKGVKVIAYDRLIR 122

Query: 120 NSGDVSYYATFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMS 179
            S +V YYATFDNFQVGVLQA S+   LGLK+GKGPFNIELFGGS DDNNAFFFY+GAMS
Sbjct: 123 GSKNVDYYATFDNFQVGVLQAQSLEKALGLKEGKGPFNIELFGGSSDDNNAFFFYNGAMS 182

Query: 180 VLKPYIDSGKLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGL 239
           VLKPYIDSGKLVV+S QMGMDKV TLRWDPATAQARMDNLLSAYYT+AKV+AVLSPYDGL
Sbjct: 183 VLKPYIDSGKLVVRSKQMGMDKVATLRWDPATAQARMDNLLSAYYTNAKVNAVLSPYDGL 242

Query: 240 SIGIISSLKGVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMV 299
           SIGI+SSL+GVGYGT  QP P VSGQDAEVPSVKSII GEQYSTIFKDTRELAKVTV MV
Sbjct: 243 SIGILSSLRGVGYGTPQQPFPYVSGQDAEVPSVKSIIRGEQYSTIFKDTRELAKVTVGMV 302

Query: 300 NAVMEGKEPEVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKEDQLK 354
           +AV+ GK+P++NDTKTY NGVKVVPSYLLKPV V K N+K+VLV  GYY E QLK
Sbjct: 303 DAVLGGKQPQINDTKTYNNGVKVVPSYLLKPVVVDKSNWKEVLVGSGYYTEAQLK 357


Lambda     K      H
   0.314    0.133    0.372 

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: 543
Number of extensions: 14
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: 354
Length of database: 357
Length adjustment: 29
Effective length of query: 325
Effective length of database: 328
Effective search space:   106600
Effective search space used:   106600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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