GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Mesorhizobium ciceri WSM1271

Align Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate YP_004144758.1 Mesci_5616 ABC transporter

Query= TCDB::Q9HU32
         (257 letters)



>NCBI__GCF_000185905.1:YP_004144758.1
          Length = 270

 Score =  317 bits (813), Expect = 1e-91
 Identities = 156/250 (62%), Positives = 199/250 (79%)

Query: 4   ATPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQ 63
           A  A+ +++LHK++G L VLKG+SL+ARDGDV++I+G SGSGKST LRCIN LENP  G 
Sbjct: 17  AAEAIHVQDLHKKFGALHVLKGVSLSARDGDVVAIIGGSGSGKSTLLRCINCLENPTSGV 76

Query: 64  ILVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVL 123
           I V+GEE+RLK   NG  + AD +QI R+RS LG VFQ+FNLW HM++++NVIE P  VL
Sbjct: 77  IRVNGEEIRLKPDGNGSTLPADRKQIERVRSRLGMVFQSFNLWTHMTLIENVIEVPVHVL 136

Query: 124 GKSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSA 183
           G  +  AI  AE LLA+VG+ +KRH YPA LSGGQQQR AIAR LA+QP+V+LFDEPTS+
Sbjct: 137 GVKREMAIIEAEKLLARVGLLEKRHVYPAFLSGGQQQRGAIARALAVQPRVMLFDEPTSS 196

Query: 184 LDPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFEN 243
           LDPE++ EVL VI  LA EGRTM+LVTHEM FAR+V++ VVFLH+G VEE+G+P  +F +
Sbjct: 197 LDPELIGEVLGVIGDLAREGRTMILVTHEMKFAREVATRVVFLHEGRVEEEGSPDAIFGS 256

Query: 244 PQSARCKQFM 253
           P+S R +QF+
Sbjct: 257 PKSERLQQFI 266


Lambda     K      H
   0.317    0.133    0.367 

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: 198
Number of extensions: 4
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: 257
Length of database: 270
Length adjustment: 25
Effective length of query: 232
Effective length of database: 245
Effective search space:    56840
Effective search space used:    56840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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