Alignments for a candidate for H281DRAFT_01113 in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Trichormus variabilis ATCC 29413

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_011318959.1 AVA_RS10980 sugar ABC transporter ATP-binding protein

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



>NCBI__GCF_000204075.1:WP_011318959.1
          Length = 517

 Score =  333 bits (854), Expect = 9e-96
 Identities = 185/509 (36%), Positives = 306/509 (60%), Gaps = 15/509 (2%)

Query: 5   EVSSAPLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGA 64
           + S    + P LE+ G+ KRF GV AL+GV+L+   G+++ L+GENG GKSTL+KI++GA
Sbjct: 8   DFSPPATATPVLEMQGIAKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGA 67

Query: 65  QPPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRL 124
              DEG++ I G          A  AGI  +YQ+L++ PN++V EN+ + SEL       
Sbjct: 68  YIADEGEIRINGKGVKITDPGTARQAGINLIYQELNVAPNLTVTENIFMGSELTR----- 122

Query: 125 ARTFDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMD 184
            +  DR+ +   A + L ++G    S   + ++  L +A +Q V IARA+   ++ ++MD
Sbjct: 123 GQFLDRKAMELEAQQVLASLGA---SFAPTDIVGTLAIAEQQQVEIARALKDNSRILVMD 179

Query: 185 EPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIA 244
           EPT +L+ +E + L  V+  LR  G+ ++++SH+++E YA+   + VLRDGQ +      
Sbjct: 180 EPTAALSDRETERLFEVIRKLRNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLTRE 239

Query: 245 EFTKAQISELMTGRHLSN--ERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGV 302
           E +  ++ ++M GR + +  E  R+S +   +VL+VR  +   +    SF+L  GEILG+
Sbjct: 240 EISPQRLVQMMVGRSMQDFYEHQRQS-NPGPVVLEVRNISDGRKVQPASFQLRAGEILGL 298

Query: 303 TGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFL 362
            GL+ +GR E++R + G     SG+V L+G+++ + +PSDA    IGYVPEDR ++GLFL
Sbjct: 299 AGLVGAGRTEVSRLIFGADRKVSGEVFLNGKKLEIHSPSDAIAVGIGYVPEDRKDQGLFL 358

Query: 363 DKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQR 422
           +   R N+    +    +  G ++      +A   V+   I    ++     LSGGNQQ+
Sbjct: 359 EMSSRKNIGLNRLKQDAN-LGIVNWGSVNKIATDAVENFHIRLANLEIRAVDLSGGNQQK 417

Query: 423 VLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCD 482
           +L+ RWLAI+PRVL+L  PT GVD+G+K  IYRI+  LS +G+ I+++S +LPE++   D
Sbjct: 418 LLLARWLAINPRVLMLDEPTRGVDIGAKSEIYRIISDLSAQGVAILMVSSELPEIVGLSD 477

Query: 483 RILMMKKGHVSAEYR---ADELSEADLYH 508
           R+L+M++G +  E       E+++ ++ H
Sbjct: 478 RVLVMREGQLVGELDNSIGKEITQENIMH 506



 Score = 70.9 bits (172), Expect = 1e-16
 Identities = 57/244 (23%), Positives = 116/244 (47%), Gaps = 11/244 (4%)

Query: 275 VLDVRGFTR----AGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLL 330
           VL+++G  +          V+  ++ GE+  + G   +G++ L + LAG   A  G++ +
Sbjct: 18  VLEMQGIAKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGAYIADEGEIRI 77

Query: 331 DGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRA 390
           +G+ + +  P  A++  I  + ++ LN    L   + +N+    + S   R   +DR   
Sbjct: 78  NGKGVKITDPGTARQAGINLIYQE-LNVAPNLT--VTENIF---MGSELTRGQFLDRKAM 131

Query: 391 QALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSK 450
           +  A+Q +  L  +    D  V +L+   QQ+V I R L  + R+L++  PT  +     
Sbjct: 132 ELEAQQVLASLGASFAPTDI-VGTLAIAEQQQVEIARALKDNSRILVMDEPTAALSDRET 190

Query: 451 DIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHAL 510
           + ++ ++++L   GI II IS  + E+    DRI +++ G        +E+S   L   +
Sbjct: 191 ERLFEVIRKLRNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLTREEISPQRLVQMM 250

Query: 511 LSEA 514
           +  +
Sbjct: 251 VGRS 254


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: 582
Number of extensions: 29
Number of successful extensions: 10
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: 517
Length adjustment: 35
Effective length of query: 480
Effective length of database: 482
Effective search space:   231360
Effective search space used:   231360
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 Apr 09 2024. 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 2024 update 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