GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Sinorhizobium meliloti 1021

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 SM_b21138 SM_b21138 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q9HU32
         (257 letters)



>FitnessBrowser__Smeli:SM_b21138
          Length = 255

 Score =  246 bits (628), Expect = 3e-70
 Identities = 128/251 (50%), Positives = 176/251 (70%), Gaps = 1/251 (0%)

Query: 5   TPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQI 64
           T  LEIR+LHKRYG +EVLKG+  + R G+VISI+GSSGSGK+T LRCIN+LE    G I
Sbjct: 2   TNLLEIRDLHKRYGTVEVLKGVDCSMRQGEVISIIGSSGSGKTTMLRCINMLEEFQGGTI 61

Query: 65  LVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLG 124
            + G+E+  + +  G       ++I R R+  G  FQ FNL+PHM+   NV+    +V  
Sbjct: 62  AIDGQEIGYETA-GGARRRKPEREIARQRALTGMAFQQFNLFPHMTAAANVMLGLVKVKK 120

Query: 125 KSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSAL 184
            S+ EA  +AE  L +VG+  ++  YP QLSGGQQQR AIAR +AM PK++LFDE TSAL
Sbjct: 121 MSRDEARVLAEKWLDRVGLLSRKDHYPGQLSGGQQQRVAIARAIAMNPKLMLFDEVTSAL 180

Query: 185 DPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENP 244
           DPE+V EVL VI+ LAE+G +ML+VTHEM FA +VSS V+F++QG + E+G P+++F  P
Sbjct: 181 DPELVNEVLQVIKGLAEDGMSMLIVTHEMRFAYEVSSRVIFMNQGRIGEEGHPREMFLKP 240

Query: 245 QSARCKQFMSS 255
           ++ R  +F+ +
Sbjct: 241 RTERLAEFLKT 251


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: 195
Number of extensions: 8
Number of successful extensions: 2
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: 255
Length adjustment: 24
Effective length of query: 233
Effective length of database: 231
Effective search space:    53823
Effective search space used:    53823
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 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