GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Rhodobacter viridis JA737

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_110805507.1 C8J30_RS08980 ABC transporter ATP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_2560
         (259 letters)



>NCBI__GCF_003217355.1:WP_110805507.1
          Length = 263

 Score =  204 bits (520), Expect = 1e-57
 Identities = 112/242 (46%), Positives = 150/242 (61%), Gaps = 3/242 (1%)

Query: 12  VFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAP 71
           VFET  G   QAL+ V+  +   DFV+ +GPSGCGK+T LR +A L+H TSG + ++  P
Sbjct: 18  VFETNDGP-VQALKDVNLSIERGDFVSFIGPSGCGKTTFLRCIAALEHPTSGTLKVNSIP 76

Query: 72  VEGPGAER--GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFE 129
            +     R  G VFQ+  L+PW TI  N++  L   G  +A+Q+ER    ++ V L GF 
Sbjct: 77  PDEARKARSYGYVFQAAGLYPWRTIAGNVKLPLEIMGYSKAEQEERVRKVLSLVDLEGFA 136

Query: 130 QHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTV 189
           + FP QLSGGMQQR +IARALA D  ILLMDEPFGALD   R  + E LL +W    KT+
Sbjct: 137 KKFPWQLSGGMQQRASIARALAFDADILLMDEPFGALDEIVRDRLNEELLKLWARTGKTI 196

Query: 190 LFVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEFMDLKARLTEEI 249
            FVTH I EA++++ ++ V S RPGRI   +   LP  R   I+ S EF+ +  R+ E +
Sbjct: 197 GFVTHSIPEAVYLSTKIVVMSPRPGRITDVIESTLPKERPLDIRDSEEFLKIAHRVREGL 256

Query: 250 RA 251
           RA
Sbjct: 257 RA 258


Lambda     K      H
   0.322    0.136    0.394 

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: 169
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: 259
Length of database: 263
Length adjustment: 25
Effective length of query: 234
Effective length of database: 238
Effective search space:    55692
Effective search space used:    55692
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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