Alignments for a candidate for H281DRAFT_01113 in Dethiosulfovibrio salsuginis USBA 82

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Dethiosulfovibrio salsuginis USBA 82

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_085544213.1 B9Y55_RS04705 ABC transporter ATP-binding protein

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



>NCBI__GCF_900177735.1:WP_085544213.1
          Length = 505

 Score =  251 bits (641), Expect = 4e-71
 Identities = 167/489 (34%), Positives = 262/489 (53%), Gaps = 23/489 (4%)

Query: 16  LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75
           L + G+ K F    A+  +S+  + G I+ ++GENG GKST++K I G   PD G++ ++
Sbjct: 4   LSIKGLTKTFGPFVAVDDISVDIKGGTIHAVVGENGAGKSTIMKCIYGIHHPDRGEISMD 63

Query: 76  GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135
           G P    S  +A+A+GI  V+Q   L+P+MSV  NV L  E           FD     +
Sbjct: 64  GKPLYIRSPRDAMASGIGMVHQHFMLVPSMSVCRNVVLGDEPVK-----GLAFDLNRARS 118

Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195
              R +E  GL  + +     +  LP+  +Q V I + +  +A+ +I DEPT  L+ KEV
Sbjct: 119 EVFRLIELYGLDISPDVP---VGTLPVGLQQQVEILKLLYRQAEVLIFDEPTAVLSPKEV 175

Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255
             L   L   +  G TV+F++H L E   I   + V+R G  +   P +E  K+ ++ELM
Sbjct: 176 GRLFETLRGFKDAGKTVIFIAHNLGEVLDISDNISVMRKGSLIDTRPASELDKSSLAELM 235

Query: 256 TGRHLSNERYRES-AHAQDIVLDVRGFTRAGQ----FSDVSFKLHGGEILGVTGLLDSGR 310
            GR ++     +    ++  +L++ G + AG       DVS K+HGGE+LGV G+  +G+
Sbjct: 236 VGRAINLPSVTDGPVLSKTPLLELSGISVAGDSRPLLDDVSLKIHGGEVLGVAGITGNGQ 295

Query: 311 NELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHR---IGYVPEDRLNEGLFLDKPIR 367
           +EL   ++G+  +  G V++DG  +   T SD+ R R   + Y+PEDRL  GL     + 
Sbjct: 296 SELEEVISGLRES-DGTVVIDGVDL---TSSDSHRRRESGLAYIPEDRLKTGLAPLASLA 351

Query: 368 DNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQS--LSGGNQQRVLI 425
           DN +       R R G   + RA++L+       +       + VQS  LSGGN QR+++
Sbjct: 352 DNGLMGYQYQDRFRNGPF-QNRAESLSHIDGIMDKYGVAAAHRAVQSGTLSGGNMQRLVM 410

Query: 426 GRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRIL 485
           GR L  DP+VL++  PT GVD+G  + I+R +  L  RG  ++LIS DL E+L   DR+ 
Sbjct: 411 GRELEHDPKVLVVSQPTRGVDIGGAEEIHRHILDLRSRGSAVLLISSDLEEVLSLSDRVA 470

Query: 486 MMKKGHVSA 494
           +M +G + A
Sbjct: 471 VMFRGKIVA 479



 Score = 72.4 bits (176), Expect = 4e-17
 Identities = 62/243 (25%), Positives = 112/243 (46%), Gaps = 11/243 (4%)

Query: 276 LDVRGFTRA-GQF---SDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLD 331
           L ++G T+  G F    D+S  + GG I  V G   +G++ + + + G+     G++ +D
Sbjct: 4   LSIKGLTKTFGPFVAVDDISVDIKGGTIHAVVGENGAGKSTIMKCIYGIHHPDRGEISMD 63

Query: 332 GQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQ 391
           G+ + +R+P DA    IG V +  +   L     +  NV+      ++     ++R R++
Sbjct: 64  GKPLYIRSPRDAMASGIGMVHQHFM---LVPSMSVCRNVVLGD-EPVKGLAFDLNRARSE 119

Query: 392 ALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKD 451
                 +  L I+    D PV +L  G QQ+V I + L     VLI   PT  +      
Sbjct: 120 VFRLIELYGLDISP---DVPVGTLPVGLQQQVEILKLLYRQAEVLIFDEPTAVLSPKEVG 176

Query: 452 IIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHALL 511
            ++  ++     G  +I I+ +L E+L   D I +M+KG +     A EL ++ L   ++
Sbjct: 177 RLFETLRGFKDAGKTVIFIAHNLGEVLDISDNISVMRKGSLIDTRPASELDKSSLAELMV 236

Query: 512 SEA 514
             A
Sbjct: 237 GRA 239



 Score = 58.9 bits (141), Expect = 4e-13
 Identities = 62/272 (22%), Positives = 118/272 (43%), Gaps = 33/272 (12%)

Query: 1   MNQQEVSSAPL--SQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLI 58
           +N   V+  P+    P LE+ G+         L  VSL    G++  + G  G G+S L 
Sbjct: 240 INLPSVTDGPVLSKTPLLELSGISVAGDSRPLLDDVSLKIHGGEVLGVAGITGNGQSELE 299

Query: 59  KIISGAQPPDEGQLVIEGVPHARLSALEALAAGIETVYQD---LSLLPNMSVAENVALTS 115
           ++ISG +  D G +VI+GV      +     +G+  + +D     L P  S+A+N  +  
Sbjct: 300 EVISGLRESD-GTVVIDGVDLTSSDSHRRRESGLAYIPEDRLKTGLAPLASLADNGLMGY 358

Query: 116 EL------------ATHEGRLARTFDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLA 163
           +             A     +    D+  +AA A RA+++  L G +             
Sbjct: 359 QYQDRFRNGPFQNRAESLSHIDGIMDKYGVAA-AHRAVQSGTLSGGN------------- 404

Query: 164 TRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECY 223
             Q + + R +  + K +++ +PT  +     + +   + +LR++G  VL +S  L+E  
Sbjct: 405 -MQRLVMGRELEHDPKVLVVSQPTRGVDIGGAEEIHRHILDLRSRGSAVLLISSDLEEVL 463

Query: 224 AIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255
           ++   V V+  G+ +A     E T+ ++  +M
Sbjct: 464 SLSDRVAVMFRGKIVALLSSKEATRDRVGRIM 495


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: 623
Number of extensions: 34
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 515
Length of database: 505
Length adjustment: 34
Effective length of query: 481
Effective length of database: 471
Effective search space:   226551
Effective search space used:   226551
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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