GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Rhizobium freirei PRF 81

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_004112627.1 RHSP_RS07985 ABC transporter ATP-binding protein

Query= uniprot:A0A165KQ08
         (355 letters)



>NCBI__GCF_000359745.1:WP_004112627.1
          Length = 371

 Score =  369 bits (948), Expect = e-107
 Identities = 200/371 (53%), Positives = 250/371 (67%), Gaps = 26/371 (7%)

Query: 5   LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64
           L I+G+ KR+G    S+E+L+ +D+ +  G FL+LVGPSGCGKSTLLN IAGL+  TEG+
Sbjct: 4   LQISGLRKRYG----SLEILKGIDLDLEQGGFLVLVGPSGCGKSTLLNTIAGLESITEGD 59

Query: 65  IRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAA 124
           IR+   ++  + P  RDIAMVFQSYALYP ++VA NI F +EMR +P  ER+  I++VA 
Sbjct: 60  IRVDDHSIADLHPSKRDIAMVFQSYALYPNMTVAGNIAFGMEMRGVPAEERKAAIEKVAK 119

Query: 125 MLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRL 184
           +LQI HLLDR+PSQLSGGQRQRVAMGRAL R P+LFLFDEPLSNLDAKLRV+MR EIKRL
Sbjct: 120 VLQIGHLLDRKPSQLSGGQRQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVDMRIEIKRL 179

Query: 185 HQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTM 244
           HQ++G T VYVTHDQ+EAMTL ++IAVMK GVVQQ GTP EIYN PAN +VA F+GSP M
Sbjct: 180 HQSTGKTIVYVTHDQIEAMTLATKIAVMKDGVVQQFGTPAEIYNNPANMFVADFMGSPAM 239

Query: 245 NLLRGAVTGGQFGI-------QGAALNL-------APPPSSANEVLLGVRPEHLVMQETA 290
           NLL G +  G  G+        GAA+ L       A    +  +V+ G+RPE L   E A
Sbjct: 240 NLLSGTIERGSNGLLVSLDRAAGAAIKLPVATDKQALEAHAGRQVVFGIRPEALTDPEGA 299

Query: 291 PWRGR--------VSVVEPTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHA 342
               R        + VVEP G DT+ +       V  R  A  R+  G+H  LA     A
Sbjct: 300 DRNARTLAENDCLIEVVEPAGSDTFAVTKLGGKEVVARLRADARISAGQHARLAFNLDKA 359

Query: 343 HWFDAQSEERL 353
            +FD Q++ R+
Sbjct: 360 VFFDPQTQARI 370


Lambda     K      H
   0.318    0.135    0.388 

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: 373
Number of extensions: 12
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: 355
Length of database: 371
Length adjustment: 29
Effective length of query: 326
Effective length of database: 342
Effective search space:   111492
Effective search space used:   111492
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: 49 (23.5 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