GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Acidovorax sp. GW101-3H11

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 Ac3H11_3200 Amino acid ABC transporter permease protein

Query= TCDB::Q9HU32
         (257 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3200
          Length = 604

 Score =  248 bits (633), Expect = 2e-70
 Identities = 131/245 (53%), Positives = 171/245 (69%), Gaps = 1/245 (0%)

Query: 10  IRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQILVSGE 69
           I  + KRYG LEVLK ++LT   G V  ILG SGSGKST LR IN LE    G I + GE
Sbjct: 358 IHGVSKRYGALEVLKDVTLTVLPGSVTVILGPSGSGKSTLLRSINHLERVDGGFIAIDGE 417

Query: 70  ELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLGKSKAE 129
            +  ++  +  L       I + R ++G VFQNFNL+PH+++L+N++EAP  V   ++AE
Sbjct: 418 LIGYRQDADA-LYELGENDILKRRVDVGMVFQNFNLFPHLTVLENIVEAPVTVRKLARAE 476

Query: 130 AIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDPEMV 189
           A  +A  LLA+VG++DK HSYP QLSGGQQQR AIAR LA++PKV+LFDEPTSALDPE+V
Sbjct: 477 AEALALELLARVGLSDKAHSYPRQLSGGQQQRVAIARALALKPKVLLFDEPTSALDPELV 536

Query: 190 QEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENPQSARC 249
            EVL+VI+ LA  G T+++VTHE+ FAR+V+  VVF+ QG V E GTP +VF  P   R 
Sbjct: 537 GEVLDVIKELARTGTTLVIVTHEIGFAREVADTVVFMEQGRVVETGTPAKVFSQPDHPRT 596

Query: 250 KQFMS 254
             F++
Sbjct: 597 AAFLA 601


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: 300
Number of extensions: 4
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: 604
Length adjustment: 31
Effective length of query: 226
Effective length of database: 573
Effective search space:   129498
Effective search space used:   129498
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 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