GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components

Query= TCDB::Q9HU32
         (257 letters)



>FitnessBrowser__Cola:Echvi_1022
          Length = 345

 Score =  142 bits (357), Expect = 1e-38
 Identities = 83/248 (33%), Positives = 142/248 (57%), Gaps = 18/248 (7%)

Query: 8   LEIRNLHKRYGDLE--VLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQIL 65
           L++  + K++   +   +K I +   +G V +I+G +GSGK+T L+ I  LE+P +G+I+
Sbjct: 4   LQLHGISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKGEIV 63

Query: 66  VSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLGK 125
            SG+ +      NG      +Q+      E+G +FQ + L+P M++L+NV EA    L +
Sbjct: 64  FSGQTI-----VNGKSALPANQR------EVGVIFQEYALFPQMTLLENVREA----LHQ 108

Query: 126 SKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSALD 185
               A +IA   LA  G+ D   +YP QLS GQ+QRAA+AR LA +PK++L D+P  +LD
Sbjct: 109 ESRNARQIAMDSLALAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLD 168

Query: 186 PEMVQEVLNVIRALAE-EGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENP 244
                E+   IR + +  G T ++ +H    A  ++  +  LH+G++++ GTP ++++ P
Sbjct: 169 TRFKNEISEDIRDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKP 228

Query: 245 QSARCKQF 252
            +A    F
Sbjct: 229 ANAYVANF 236


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: 191
Number of extensions: 10
Number of successful extensions: 4
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: 345
Length adjustment: 26
Effective length of query: 231
Effective length of database: 319
Effective search space:    73689
Effective search space used:    73689
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: 48 (23.1 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