GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03640 in Caulobacter crescentus NA1000

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__Caulo:CCNA_00903
          Length = 515

 Score =  405 bits (1041), Expect = e-117
 Identities = 230/503 (45%), Positives = 324/503 (64%), Gaps = 9/503 (1%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           LL +  + KSF    AL  + L +  GE+HAL+GENGAGKSTL+K+LS  HA D G +  
Sbjct: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62

Query: 66  DGRPVALRD-PGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124
            G+ +  RD P   +  GI  IYQE  + P +SVA N+++G E R RLGL+D + +R+  
Sbjct: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPR-RLGLVDWSRLRADA 121

Query: 125 DAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184
            A+L  LG           L++AEQQ VEIA+A+   +R++IMDEPTAALS RE ++L  
Sbjct: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181

Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 244
           ++  L+   +++IY+SHR+ EV A+ DR TV+RDG FV      +++   +V++MVGR +
Sbjct: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241

Query: 245 SEFYQHQRIAPADAAQLP----TVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTE 300
            EF + +R  P  A  L     T    R  A G +R  SF  R GE++G AGLVGAGRT+
Sbjct: 242 -EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300

Query: 301 LARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM 360
           LARL+FGADP + G +L++ +P+ +  PR A++AGI  VPEDRK QG FL  ++  N ++
Sbjct: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360

Query: 361 NVASRHTRLGL-VRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIA 419
                 + LG  V  R+   +     Q+L +K+A  ET +GKLSGGNQQKVLL R + + 
Sbjct: 361 PSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420

Query: 420 PKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMI 479
           PKVLI+DEPTRG+DI AK+E++Q++  LA  GVAVVVISSEL EV+ + DR++V REG+I
Sbjct: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480

Query: 480 TGELAGAAITQENIMR-LATDTN 501
             +L     T+E +M  +AT T+
Sbjct: 481 VADLDAQTATEEGLMAYMATGTD 503



 Score = 85.9 bits (211), Expect = 3e-21
 Identities = 64/222 (28%), Positives = 111/222 (50%), Gaps = 7/222 (3%)

Query: 282 VRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHI-DQPRAAMRAGIAYVP 340
           V  GEV    G  GAG++ L ++L  A     G +   G+ +   D P    + GIA + 
Sbjct: 26  VGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQQLGIATIY 85

Query: 341 EDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVG 400
           ++     LF +++VA N  M +     RLGLV    L   A+A +  L + + +P+ PV 
Sbjct: 86  QEFN---LFPELSVAEN--MYLGREPRRLGLVDWSRLRADAQALLNDLGLPL-NPDAPVR 139

Query: 401 KLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSE 460
            L+   QQ V +A+ + +  +++I+DEPT  +       ++ ++  L ++ V+V+ +S  
Sbjct: 140 GLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSHR 199

Query: 461 LPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNV 502
           L EV  +CDR  VMR+G        A +   +++RL    +V
Sbjct: 200 LGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241


Lambda     K      H
   0.320    0.135    0.378 

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: 743
Number of extensions: 41
Number of successful extensions: 9
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: 521
Length of database: 515
Length adjustment: 35
Effective length of query: 486
Effective length of database: 480
Effective search space:   233280
Effective search space used:   233280
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 (21.8 bits)
S2: 52 (24.6 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