GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Microvirga lotononidis WSM3557

Align CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_040638722.1 MICLODRAFT_RS20885 sugar ABC transporter substrate-binding protein

Query= TCDB::P25548
         (354 letters)



>NCBI__GCF_000262405.1:WP_040638722.1
          Length = 347

 Score =  549 bits (1415), Expect = e-161
 Identities = 273/347 (78%), Positives = 305/347 (87%)

Query: 8   MAACAIGAASFAAPAFAQDKGSVGIAMPTKSSARWIDDGNNIVKQLQEAGYKTDLQYADD 67
           MAA A+GA      A AQDKG+VG+AMPTKSSARWIDDGNN+VK L+E GY  DLQYA+D
Sbjct: 1   MAAVALGAFGLIGAAQAQDKGTVGVAMPTKSSARWIDDGNNMVKVLKEKGYNVDLQYAED 60

Query: 68  DIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIRNSGDVSYY 127
           DIPNQLSQIENM+TKG KVLVIA+IDGTTLSD L+QA ++GIKVIAYDRLIRNS +V YY
Sbjct: 61  DIPNQLSQIENMITKGSKVLVIAAIDGTTLSDALQQAADKGIKVIAYDRLIRNSKNVDYY 120

Query: 128 ATFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMSVLKPYIDS 187
           ATFDNFQVGVLQ   I   LGLK+GKGPFNIELFGGSPDDNNA+FFY+GAMSVL+PYI S
Sbjct: 121 ATFDNFQVGVLQGGYIEKALGLKEGKGPFNIELFGGSPDDNNAYFFYNGAMSVLEPYIKS 180

Query: 188 GKLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGLSIGIISSL 247
           GKL V SGQ GMDKV TLRWD A AQARMDNLLSAYYTD +VDAVLSPYDGLSIGIISSL
Sbjct: 181 GKLKVVSGQTGMDKVSTLRWDGAVAQARMDNLLSAYYTDKRVDAVLSPYDGLSIGIISSL 240

Query: 248 KGVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMVNAVMEGKE 307
           KGVGYGT  QP+P+++GQDAEVPS+KSI+A EQ ST+FKDTRELAKVTVNMV+AV+ GK+
Sbjct: 241 KGVGYGTPKQPMPIITGQDAEVPSIKSILAKEQTSTVFKDTRELAKVTVNMVDAVLSGKQ 300

Query: 308 PEVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKEDQLK 354
           PEVNDTKTYENGVKVVP+YLLKPV+V   N+K++LV  GYYKEDQ K
Sbjct: 301 PEVNDTKTYENGVKVVPAYLLKPVSVDASNWKEILVGSGYYKEDQFK 347


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: 16
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: 347
Length adjustment: 29
Effective length of query: 325
Effective length of database: 318
Effective search space:   103350
Effective search space used:   103350
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 24 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