GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Acidovorax sp. GW101-3H11

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

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2066
          Length = 355

 Score =  344 bits (883), Expect = 2e-99
 Identities = 188/373 (50%), Positives = 242/373 (64%), Gaps = 31/373 (8%)

Query: 2   ATLELRNVNKTYGPG--LPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISG 59
           ++L++  +NK +G G    + L+ +++ +  GEFLILVGPSGCGKSTL+N IAGL+  + 
Sbjct: 3   SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62

Query: 60  GAILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARV 119
           G I +   ++ GM P+DRDIAMVFQSYALYPT+SV DNI F L++RKMP  E  + +  V
Sbjct: 63  GEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122

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

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

Query: 240 PMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGL-------EDREVILGIRPEQII 292
            MN            L   +  GQ       G+Q A L          EV+LG+RPE ++
Sbjct: 243 TMNL-----------LRGAVTGGQ------FGIQGAALNLAPPPSSANEVLLGVRPEHLV 285

Query: 293 LANGEANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPA 352
           +           R  V V EPTGPDT V V+     V  R         GE + L   PA
Sbjct: 286 MQE-----TAPWRGRVSVVEPTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPA 340

Query: 353 KVLLFDAKTGERL 365
               FDA++ ERL
Sbjct: 341 HAHWFDAQSEERL 353


Lambda     K      H
   0.319    0.138    0.393 

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: 437
Number of extensions: 17
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 ( 7.4 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