GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Caulobacter crescentus NA1000

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__Caulo:CCNA_00903
          Length = 515

 Score =  126 bits (316), Expect = 1e-33
 Identities = 76/243 (31%), Positives = 134/243 (55%), Gaps = 13/243 (5%)

Query: 9   VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68
           +L V+ +SK F G++AL  V + +  G+V+ L+G NGAGK+T   +++  +  DAGT   
Sbjct: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62

Query: 69  AGKPYEPT-AVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGF 127
           AG+  +P  A     + GIA  +Q   LF E++  EN+ +GR  R      G V      
Sbjct: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRR----LGLV------ 112

Query: 128 KAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAG 187
             + + +   AQ LL+ +G+    D   R L+  +Q+ +EIA+A+  + +LI +DEP A 
Sbjct: 113 --DWSRLRADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAA 170

Query: 188 MNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKN 247
           ++  E  +L  +I  ++  + +++ + H +  V  +CDR TV+  G+ +A G+ A+V+  
Sbjct: 171 LSGREVDRLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVA 230

Query: 248 EKV 250
           + V
Sbjct: 231 DMV 233



 Score = 69.7 bits (169), Expect = 1e-16
 Identities = 65/259 (25%), Positives = 117/259 (45%), Gaps = 20/259 (7%)

Query: 8   VVLKVAGISKRFGGLQA---LSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAG 64
           VVLKV G++     L A   L  V    + G++ GL G  GAG+T    +I G     AG
Sbjct: 255 VVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAG 314

Query: 65  TFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGL-----FG 119
              +  KP    +  +  +AGI        L  E    +   +   IR    L       
Sbjct: 315 RVLVDDKPLRLRSPRDAIQAGIM-------LVPEDRKQQGCFLDHSIRRNLSLPSLKALS 367

Query: 120 AVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLI 179
           A+ +    +AE   +    Q+L   +   + A  K   LS G+Q+++ + RA+A  P+++
Sbjct: 368 ALGQWVDERAERDLVETYRQKLRIKMADAETAIGK---LSGGNQQKVLLGRAMALTPKVL 424

Query: 180 ALDEPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEG 239
            +DEP  G++   K ++ +++  + +    +++I  ++  VM + DR+ V   G  +A+ 
Sbjct: 425 IVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADL 484

Query: 240 NPAEVQKNEKVIEAYLGTG 258
           +       E+ + AY+ TG
Sbjct: 485 DAQTA--TEEGLMAYMATG 501


Lambda     K      H
   0.319    0.137    0.384 

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: 304
Number of extensions: 21
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 260
Length of database: 515
Length adjustment: 29
Effective length of query: 231
Effective length of database: 486
Effective search space:   112266
Effective search space used:   112266
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