GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Caulobacter crescentus NA1000

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>FitnessBrowser__Caulo:CCNA_01670
          Length = 339

 Score =  157 bits (397), Expect = 4e-43
 Identities = 117/327 (35%), Positives = 171/327 (52%), Gaps = 33/327 (10%)

Query: 1   MQLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVT 60
           M +A+ S+ K+ G    L  + L +  G +  LLG + +GKT+L+R +AGL+ P AG+V 
Sbjct: 1   MTIAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVL 60

Query: 61  VDGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKN------IDARVREI 114
            DG+DVT      R V  V+QQ+  +  M VA NIA  L +R  K+      I  RV E+
Sbjct: 61  FDGQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEEL 120

Query: 115 ASRLHIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELT 174
              + ++    RYP++LSGGQ+QRVAL+RALA    ++LLDEP   LD  +R+ LR EL 
Sbjct: 121 LKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELR 180

Query: 175 QLFAAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDP 234
           ++  A   T ++ T +  EAL L    A+L+ G++ Q G   +V  AP +  V     + 
Sbjct: 181 RVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVGE- 239

Query: 235 PMNLMAASATAQGVRLQGGAELTLP---LPQGAATAAGLTVGVRASALRVHARPGDVSV- 290
                       G R + GA LT+P   L  GAATA              + RP D ++ 
Sbjct: 240 ---ANRFDGQVSGGRFKAGA-LTVPASALKDGAATA--------------YVRPHDFALD 281

Query: 291 -AG---VVELAEISGSDTFVHASTPWG 313
            AG   ++E A++ G+ T V A T  G
Sbjct: 282 EAGFEVLIERAQVQGALTAVTALTSDG 308


Lambda     K      H
   0.318    0.133    0.375 

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: 249
Number of extensions: 8
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: 363
Length of database: 339
Length adjustment: 29
Effective length of query: 334
Effective length of database: 310
Effective search space:   103540
Effective search space used:   103540
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