GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Magnetospirillum magneticum AMB-1

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_011383734.1 AMB_RS06730 nitrate ABC transporter ATP-binding protein

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



>NCBI__GCF_000009985.1:WP_011383734.1
          Length = 452

 Score =  206 bits (524), Expect = 7e-58
 Identities = 109/257 (42%), Positives = 160/257 (62%), Gaps = 4/257 (1%)

Query: 4   VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63
           + ++ V + F T   +    L+ VDF++ + + V +LG SG GKSTLLRI+AGL  A  G
Sbjct: 11  LDLRGVRKTFLTPDRRERTVLEGVDFKLEEGEIVALLGKSGSGKSTLLRIMAGLIKANGG 70

Query: 64  RVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKV 123
            V   G  + GP     MVFQS+ LFPWLT+E+N+  GL   G+ +A+++ERA   I  +
Sbjct: 71  EVKYRGHLMTGPAKGISMVFQSFALFPWLTVEENVELGLEAAGVAKAEREERANEAIDLI 130

Query: 124 GLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWE 183
           GL G+E  +PK+LSGGM+QR   ARAL   P +LL+DEPF ALD  T   ++E LL +W+
Sbjct: 131 GLGGYESAYPKELSGGMRQRVGFARALVMRPDVLLLDEPFSALDVLTSETLREDLLELWD 190

Query: 184 AER---KTVLFVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEFMD 240
             +   K +L V+H+I+EA+ MA+RV VFS+ PGR++ E+ V+LP PR        + +D
Sbjct: 191 ERKIPTKGILLVSHNIEEAVSMADRVLVFSSDPGRVRAEIRVNLPRPRDTESAAFRQIVD 250

Query: 241 -LKARLTEEIRAESMAA 256
            +   +T  +R   + A
Sbjct: 251 EVYTLMTANVRGGGLGA 267


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: 278
Number of extensions: 10
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: 452
Length adjustment: 29
Effective length of query: 230
Effective length of database: 423
Effective search space:    97290
Effective search space used:    97290
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: 49 (23.5 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