Alignments for a candidate for H281DRAFT_01113 in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Caulobacter crescentus NA1000

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>FitnessBrowser__Caulo:CCNA_00903
          Length = 515

 Score =  316 bits (810), Expect = 1e-90
 Identities = 192/499 (38%), Positives = 287/499 (57%), Gaps = 16/499 (3%)

Query: 16  LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75
           L+V  V K F GV AL  V L    G+++ LLGENG GKSTLIKI+S A   D G +   
Sbjct: 4   LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63

Query: 76  G-VPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLA 134
           G V   R + L     GI T+YQ+ +L P +SVAEN+ L       E R     D   L 
Sbjct: 64  GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLG-----REPRRLGLVDWSRLR 118

Query: 135 ATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKE 194
           A A   L  +GLP N +     +  L +A +Q+V IA+A+   A+ +IMDEPT +L+ +E
Sbjct: 119 ADAQALLNDLGLPLNPDAP---VRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGRE 175

Query: 195 VDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISEL 254
           VD L A++A L+A+ V+V++VSH+L E  A+     V+RDG+ +A G +A+   A +  L
Sbjct: 176 VDRLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRL 235

Query: 255 MTGRHLSNERYRESAHAQDIVLDVRGFTRA-------GQFSDVSFKLHGGEILGVTGLLD 307
           M GRH+  ER +       +VL V G T A       G    VSF   GGEI+G+ GL+ 
Sbjct: 236 MVGRHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVG 295

Query: 308 SGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIR 367
           +GR +LAR + G  P  +G VL+D + + LR+P DA +  I  VPEDR  +G FLD  IR
Sbjct: 296 AGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIR 355

Query: 368 DNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGR 427
            N+    + +L      +D    + L E   ++L+I     +  +  LSGGNQQ+VL+GR
Sbjct: 356 RNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGR 415

Query: 428 WLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMM 487
            +A+ P+VLI+  PT G+D+G+K  +++++  L+  G+ +++IS +L E++   DRI++ 
Sbjct: 416 AMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVF 475

Query: 488 KKGHVSAEYRADELSEADL 506
           ++G + A+  A   +E  L
Sbjct: 476 REGVIVADLDAQTATEEGL 494



 Score = 69.3 bits (168), Expect = 3e-16
 Identities = 56/226 (24%), Positives = 103/226 (45%), Gaps = 28/226 (12%)

Query: 297 GEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDA--KRHRIGYV--- 351
           GE+  + G   +G++ L + L+    A +G V   GQ +    P DA  +R ++G     
Sbjct: 29  GEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVL---DPRDAPLRRQQLGIATIY 85

Query: 352 ------PEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIAT 405
                 PE  + E ++L +  R             R G +D +R +A A+  + +L +  
Sbjct: 86  QEFNLFPELSVAENMYLGREPR-------------RLGLVDWSRLRADAQALLNDLGLPL 132

Query: 406 PGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGI 465
              D PV+ L+   QQ V I + + ++ R++I+  PT  +     D ++ I+  L  R +
Sbjct: 133 -NPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSV 191

Query: 466 GIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHALL 511
            +I +S  L E+   CDR  +M+ G   A     ++  AD+   ++
Sbjct: 192 SVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMV 237


Lambda     K      H
   0.319    0.135    0.376 

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: 634
Number of extensions: 31
Number of successful extensions: 7
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: 515
Length of database: 515
Length adjustment: 35
Effective length of query: 480
Effective length of database: 480
Effective search space:   230400
Effective search space used:   230400
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: 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources