GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Mesorhizobium ciceri WSM1271

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate YP_004144835.1 Mesci_5725 ABC transporter

Query= TCDB::Q52666
         (263 letters)



>NCBI__GCF_000185905.1:YP_004144835.1
          Length = 246

 Score =  337 bits (865), Expect = 1e-97
 Identities = 158/244 (64%), Positives = 199/244 (81%)

Query: 20  EIAIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKI 79
           +  I+   ++KWYG F  L D+NLTV +GERIVI GPSGSGKST+IRC NRLE HQ G+I
Sbjct: 3   DTVIEAKNVSKWYGTFRALTDVNLTVRKGERIVICGPSGSGKSTLIRCFNRLEAHQEGEI 62

Query: 80  IVDGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAM 139
            V+GI L + ++++ +VR+ VGMVFQHFNLFPH+T+L N   AP+W++ + + EA++ A+
Sbjct: 63  TVNGIRLHNKMRDLAEVRTNVGMVFQHFNLFPHMTVLMNCMAAPMWIKGMSEAEAKKIAL 122

Query: 140 YYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDT 199
            +LE+V+IPEQA K+PGQLSGGQQQRVAIARSLCM+P +MLFDEPTS+LDPEM+ EVL+T
Sbjct: 123 KFLERVRIPEQANKFPGQLSGGQQQRVAIARSLCMEPAVMLFDEPTSSLDPEMVAEVLET 182

Query: 200 MIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFLSQ 259
           M  LA EGMTM+CVTHEMGFA++VA+RVIFM  G+IVE+  PHDFF  PQ ERTK FL Q
Sbjct: 183 MTSLAREGMTMVCVTHEMGFARSVADRVIFMDAGRIVEEGKPHDFFTKPQHERTKLFLHQ 242

Query: 260 ILGH 263
           IL H
Sbjct: 243 ILSH 246


Lambda     K      H
   0.320    0.134    0.391 

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: 247
Number of extensions: 9
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: 263
Length of database: 246
Length adjustment: 24
Effective length of query: 239
Effective length of database: 222
Effective search space:    53058
Effective search space used:    53058
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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