GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)

Query= reanno::WCS417:GFF4321
         (386 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2066
          Length = 355

 Score =  352 bits (902), Expect = e-101
 Identities = 190/367 (51%), Positives = 244/367 (66%), Gaps = 19/367 (5%)

Query: 2   ATLELRNVNKTYGAG--LPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITG 59
           ++L++  +NK +G G    + L+ +++ +  GEFLILVGPSGCGKSTL+N IAGL+  T 
Sbjct: 3   SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62

Query: 60  GAIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARV 119
           G I IG ++V GM P+DRDIAMVFQSYALYPT+SV +NI F L++RKMP+ +    +  V
Sbjct: 63  GEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122

Query: 120 AKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMK 179
           A +LQI HLL+R+P QLSGGQ+QRVAMGRALAR+P+++LFDEPLSNLDAKLRVEMR E+K
Sbjct: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182

Query: 180 LMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSP 239
            +HQ    T+VYVTHDQ+EAMTLG ++AVMK G++QQ GTP EIYN PAN +VA+FIGSP
Sbjct: 183 RLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSP 242

Query: 240 PMNFVPLRLQRKDGRLVALLDSGQARCE-LALNTTEAGLEDRDVILGLRPEQIMLAAGEG 298
            MN            L   +  GQ   +  ALN         +V+LG+RPE +++     
Sbjct: 243 TMNL-----------LRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVM----- 286

Query: 299 DSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFD 358
              +  R  V V EPTGPDT V V      V  R       Q GE + L   P+    FD
Sbjct: 287 QETAPWRGRVSVVEPTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFD 346

Query: 359 ANTGERL 365
           A + ERL
Sbjct: 347 AQSEERL 353


Lambda     K      H
   0.318    0.135    0.382 

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: 402
Number of extensions: 12
Number of successful extensions: 3
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: 386
Length of database: 355
Length adjustment: 30
Effective length of query: 356
Effective length of database: 325
Effective search space:   115700
Effective search space used:   115700
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 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