GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03640 in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  286 bits (732), Expect = 1e-81
 Identities = 171/499 (34%), Positives = 274/499 (54%), Gaps = 15/499 (3%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           +++M+ IRK F   +A  ++ L ++ GEIHAL+GENGAGKSTLM VL G++ P++GEIL+
Sbjct: 4   VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63

Query: 66  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125
            G+PV + DP  +   GI +++Q   +    +V  N+ +G E  T  G I+        +
Sbjct: 64  KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKE-PTAGGKINIKKAAKAVE 122

Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
            + +Q G           +S+  QQ+VEI + L   + I+I DEPTAAL+ +E  +L  +
Sbjct: 123 TISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQI 182

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245
           +++L  EG +II I+H++ E+  + DR TV+R G  +G +   E   + +  MMVGR ++
Sbjct: 183 MKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVN 242

Query: 246 EFYQHQRIAPADAAQLPTVMQVRALAGGKIRPAS------FDVRAGEVLGFAGLVGAGRT 299
              +     P DA     V+Q++ L     R  +       +V AGE+LG AG+ G G+T
Sbjct: 243 FSVEKDPAQPKDA-----VLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQT 297

Query: 300 ELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANAT 359
           EL   + G    +GG+I L G+ +    PR    AG+ ++P+DR   GL L   V  N  
Sbjct: 298 ELIEAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIV 357

Query: 360 MNV--ASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLE 417
           +       ++  G++    +   A   I+  +V+     T    LSGGNQQK ++AR ++
Sbjct: 358 LQTYYQKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVD 417

Query: 418 IAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREG 477
            +P +LI  +PTRG+D+ A   I+  + +   +G AV++IS EL EV+ + DR+ V+ EG
Sbjct: 418 RSPDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEG 477

Query: 478 MITGELAGAAITQENIMRL 496
            I   +  A  T EN + L
Sbjct: 478 KIVA-IVDADKTNENELGL 495



 Score = 90.5 bits (223), Expect = 1e-22
 Identities = 59/224 (26%), Positives = 106/224 (47%), Gaps = 6/224 (2%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338
           +  V+ GE+    G  GAG++ L  +LFG      G+IL++G+PV I  P  A R GI  
Sbjct: 24  TLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILVKGKPVKITDPNVANRLGIGM 83

Query: 339 VPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETP 398
           V      Q   L         + +    T  G +  +          ++  + V  P   
Sbjct: 84  VH-----QHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVETISKQYGLAV-DPYAK 137

Query: 399 VGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVIS 458
           +  +S G QQ+V + + L    ++LI DEPT  +     +E+ Q++ +L S+G ++++I+
Sbjct: 138 IQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQIMKKLVSEGKSIILIT 197

Query: 459 SELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNV 502
            +L E++ +CDR  V+R G   G +  +  T +++  +     V
Sbjct: 198 HKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREV 241



 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 56/230 (24%), Positives = 114/230 (49%), Gaps = 7/230 (3%)

Query: 21  ALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRA 80
           A++D+HL +  GEI  + G +G G++ L++ ++G+  P  G I L+G+ +    P     
Sbjct: 272 AVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQLNGQDITGLTPRKITG 331

Query: 81  AGINLIYQEL---AVAPNISVAANVFMGSELR---TRLGLIDHAAMRSRTDAVLRQLGAG 134
           AG+  I Q+     +  + +V  N+ + +  +   +  G+++   +  + + ++      
Sbjct: 332 AGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVLNFNEIYKKANELIEDYDVR 391

Query: 135 FGASD-LAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEG 193
             +   LA  LS   QQ+  IAR +     ++I  +PT  L     E + + + + RD+G
Sbjct: 392 TPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDVGAIESIHHRLVKERDKG 451

Query: 194 LAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 243
            A++ IS  + EV  ++DR+ V+ +G  V  +  D+ +   +  +M G S
Sbjct: 452 KAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENELGLLMAGGS 501


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: 628
Number of extensions: 35
Number of successful extensions: 9
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: 521
Length of database: 509
Length adjustment: 35
Effective length of query: 486
Effective length of database: 474
Effective search space:   230364
Effective search space used:   230364
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 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:

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:

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