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_004141781.1 Mesci_2595 ABC transporter

Query= TCDB::Q9HU32
         (257 letters)



>NCBI__GCF_000185905.1:YP_004141781.1
          Length = 669

 Score =  328 bits (841), Expect = 2e-94
 Identities = 161/250 (64%), Positives = 201/250 (80%)

Query: 5   TPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQI 64
           TPA++I  LHK +G L VLKG++LTA  G+VIS++GSSGSGKSTFLRCINLLE P  G++
Sbjct: 417 TPAVQIDELHKSFGSLLVLKGVNLTAHAGEVISMIGSSGSGKSTFLRCINLLEQPDGGKV 476

Query: 65  LVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLG 124
            + GE +++K   +G L  AD  Q+ R+R+ +G VFQNFNLWPHM++ +N+IEAPR VL 
Sbjct: 477 AIDGEVIKMKPLSSGRLGPADMAQVERIRARVGMVFQNFNLWPHMTVAENIIEAPRHVLK 536

Query: 125 KSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSAL 184
           + + +AIE A  LL KVG+ADK   YP QLSGGQQQRAAIARTLAM+PKVILFDEPTSAL
Sbjct: 537 EPREKAIEHAHALLKKVGLADKHAHYPGQLSGGQQQRAAIARTLAMRPKVILFDEPTSAL 596

Query: 185 DPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENP 244
           DPE+V EVL VIR LAEEG TM+LVTHEM FAR+VS +V+FLHQG VEE+G P ++F NP
Sbjct: 597 DPELVGEVLRVIRQLAEEGNTMILVTHEMQFAREVSHKVLFLHQGKVEEEGAPAELFGNP 656

Query: 245 QSARCKQFMS 254
           +S R +QF++
Sbjct: 657 RSERLRQFLA 666


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: 381
Number of extensions: 8
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: 669
Length adjustment: 31
Effective length of query: 226
Effective length of database: 638
Effective search space:   144188
Effective search space used:   144188
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: 50 (23.9 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