GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Caulo:CCNA_00903 CCNA_00903 inositol transport
           ATP-binding protein IatA
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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