Alignments for a candidate for araVsh in Archaeoglobus veneficus SNP6

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Archaeoglobus veneficus SNP6

Align ABC transporter related (characterized, see rationale)
to candidate WP_048086136.1 ARCVE_RS02230 ABC transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>NCBI__GCF_000194625.1:WP_048086136.1
          Length = 506

 Score =  262 bits (670), Expect = 2e-74
 Identities = 158/468 (33%), Positives = 260/468 (55%), Gaps = 3/468 (0%)

Query: 7   LKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGE 66
           ++ I K +PGV A + V+L ++ GE+H LLGENGAGK+TL+ V+ G    D G+I+F G+
Sbjct: 1   MRGIVKRFPGVVANDGVNLTVYRGEIHGLLGENGAGKTTLMNVLYGLYQPDEGEIIFEGK 60

Query: 67  PQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAVLT 126
              F +P DA +AGI  V+Q   LV  + V QN+ LGY   +  LI    +      +  
Sbjct: 61  KVRFKSPKDAIEAGIGMVHQHFMLVRRMNVLQNIVLGYRTPKDPLIDEGWVKEKINELSR 120

Query: 127 QFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQL 186
            + + +D    +++ S+  +Q + I + +  + K+L+LDEPTA L  +EV+ LF  L  +
Sbjct: 121 TYGIGVDADEVVANLSVGEEQRVEILKALFRNVKLLILDEPTAVLTPQEVKNLFSALKAM 180

Query: 187 KAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRS-LQEQL 245
             KG+ ++FITH L +   ++DRITVLR G+ +G   T++  + +L   M+GR  + E  
Sbjct: 181 TDKGLTVIFITHKLKEALSVTDRITVLRRGKNVGTIETSKTDERELARMMVGREVVMEIR 240

Query: 246 VDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVF 305
             K E    V + E   L +ED     +++ ++ ++ KG+ +G+AG+ G+G+ E+  A+ 
Sbjct: 241 KPKVELGEEVLKVED--LWVEDDRGLMALKGISFSIRKGEILGIAGVSGNGQKELEEAIA 298

Query: 306 GLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQARI 365
           GL     G I L G+ +         ++GIA  PEDR   G+   LS+ EN++L      
Sbjct: 299 GLRKPRKGKIILNGRDITNLSVEGYTASGIACIPEDRIGVGLAPSLSVAENLMLRDFRNF 358

Query: 366 GWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLVLD 425
                L     +E A+  +++  I TP  D P   LSGGN Q++ILAR L+  P LL+  
Sbjct: 359 RRGFTLDFKAMEERAKKLVEEFAIKTPSLDVPASTLSGGNIQRLILARELSRNPKLLIAS 418

Query: 426 EPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473
           +P+RG+DI     + + +      G ++L+ S +LDE++  S+ + V+
Sbjct: 419 QPSRGLDIAGIEYVRQRLIDAAKSGSAILLISEDLDEILQLSDTIAVI 466



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 54/204 (26%), Positives = 103/204 (50%), Gaps = 18/204 (8%)

Query: 277 MNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIA 336
           +NLTV +G+  GL G  G+G++ + N ++GL   D G I   G+K+    P DAI AGI 
Sbjct: 17  VNLTVYRGEIHGLLGENGAGKTTLMNVLYGLYQPDEGEIIFEGKKVRFKSPKDAIEAGIG 76

Query: 337 LCPEDRKIDGIIGPLSIRENIILALQARI------GWWRYLSNTRQQEIAQFFIDKLQIA 390
           +  +   +   +  +++ +NI+L  +         GW +   N          + +    
Sbjct: 77  MVHQHFML---VRRMNVLQNIVLGYRTPKDPLIDEGWVKEKINE---------LSRTYGI 124

Query: 391 TPDADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEG 450
             DAD+ +  LS G +Q+V + + L     LL+LDEPT  +       +   ++ + D+G
Sbjct: 125 GVDADEVVANLSVGEEQRVEILKALFRNVKLLILDEPTAVLTPQEVKNLFSALKAMTDKG 184

Query: 451 MSLLVASSELDELVAFSNKVVVLR 474
           ++++  + +L E ++ ++++ VLR
Sbjct: 185 LTVIFITHKLKEALSVTDRITVLR 208



 Score = 77.0 bits (188), Expect = 1e-18
 Identities = 57/211 (27%), Positives = 105/211 (49%), Gaps = 6/211 (2%)

Query: 16  GVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMD 75
           G+ AL+ +S  +  GE+  + G +G G+  L + + G +    G I+  G      +   
Sbjct: 263 GLMALKGISFSIRKGEILGIAGVSGNGQKELEEAIAGLRKPRKGKIILNGRDITNLSVEG 322

Query: 76  AQKAGISTVYQE---VNLVPNLTVAQNLFL-GYEPRRLGL-IHFKKMYADARAVLTQFKL 130
              +GI+ + ++   V L P+L+VA+NL L  +   R G  + FK M   A+ ++ +F +
Sbjct: 323 YTASGIACIPEDRIGVGLAPSLSVAENLMLRDFRNFRRGFTLDFKAMEERAKKLVEEFAI 382

Query: 131 DI-DVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKAK 189
               +  P S  S    Q + +AR ++ + K+L+  +P+  LD   ++ +   L      
Sbjct: 383 KTPSLDVPASTLSGGNIQRLILARELSRNPKLLIASQPSRGLDIAGIEYVRQRLIDAAKS 442

Query: 190 GVAIVFITHFLDQVYQISDRITVLRNGQFIG 220
           G AI+ I+  LD++ Q+SD I V+  G+  G
Sbjct: 443 GSAILLISEDLDEILQLSDTIAVIYEGELKG 473


Lambda     K      H
   0.319    0.136    0.377 

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: 609
Number of extensions: 37
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 499
Length of database: 506
Length adjustment: 34
Effective length of query: 465
Effective length of database: 472
Effective search space:   219480
Effective search space used:   219480
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 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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