GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Alkalihalobacterium alkalinitrilicum DSM 22532

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= uniprot:B2T9V9
         (510 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  248 bits (633), Expect = 4e-70
 Identities = 155/484 (32%), Positives = 256/484 (52%), Gaps = 16/484 (3%)

Query: 14  VVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRF 73
           V+E  ++ K F    A ++V+++V  GE HAL+G NGAGKSTL+++L GL +P+ GE+  
Sbjct: 4   VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63

Query: 74  SGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARA 133
            G          A R  +  V+QH  ++   +V EN+ + ++P  GG I+ +   +    
Sbjct: 64  KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVET 123

Query: 134 LLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRI 193
           +   + + V   A+  D+SV  +Q VEI + L  GA  +I DEPTA L   EI  L + +
Sbjct: 124 ISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQIM 183

Query: 194 SELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGL 253
            +L  EG + + I+H L+E+ E+C   TV+R  R I +  +S    + L   M G     
Sbjct: 184 KKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVNF 243

Query: 254 AVADAAARGALPADTAVALELKELTGADYEGVS------FTVKRGEVVGLTGATSSGRTS 307
           +V    A+   P D    L++K+L   D   ++        V  GE++G+ G   +G+T 
Sbjct: 244 SVEKDPAQ---PKD--AVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTE 298

Query: 308 VAEAIAGLRAAKRGTISVDGAILPPGDVPASL-AHGIGCVPKDRHHEGLVLTQSVAENAS 366
           + EAI GLR    G I ++G  +  G  P  +   G+G +P+DRH  GLVL  +V EN  
Sbjct: 299 LIEAITGLRKPTGGNIQLNGQDI-TGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIV 357

Query: 367 MT--IARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALA 424
           +     +     G+    +      ++I+   +       +   LSGGNQQK ++AR + 
Sbjct: 358 LQTYYQKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVD 417

Query: 425 TNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRG 483
            +P++L+   PT G+DV + E++   + + R++GKAVL++S ELD+ L   DR+ V++ G
Sbjct: 418 RSPDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEG 477

Query: 484 RVAA 487
           ++ A
Sbjct: 478 KIVA 481



 Score = 73.2 bits (178), Expect = 2e-17
 Identities = 61/240 (25%), Positives = 109/240 (45%), Gaps = 14/240 (5%)

Query: 20  VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79
           V K      A+ND+ + V  GE   + G +G G++ L+  +TGLRKP  G ++ +G    
Sbjct: 263 VVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQLNGQDIT 322

Query: 80  SIADRDAWRERVACV----YQHSTIIRDLSVAENLFIN---RQPLR-GGVIDWQAMRRDA 131
            +  R      V  +    ++H  ++ D +V EN+ +    ++P    GV+++  + + A
Sbjct: 323 GLTPRKITGAGVGHIPQDRHKHGLVL-DFTVGENIVLQTYYQKPYSTSGVLNFNEIYKKA 381

Query: 132 RALLDHWKIDVR---EDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKR 188
             L++ +  DVR   E   A  LS   +Q   IAR +      +I  +PT  LD   I+ 
Sbjct: 382 NELIEDY--DVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDVGAIES 439

Query: 189 LFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG 248
           +  R+ + + +G   L IS  L EV  +   + V+ + + +           +L   M G
Sbjct: 440 IHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENELGLLMAG 499


Lambda     K      H
   0.318    0.134    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: 567
Number of extensions: 40
Number of successful extensions: 9
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: 510
Length of database: 509
Length adjustment: 34
Effective length of query: 476
Effective length of database: 475
Effective search space:   226100
Effective search space used:   226100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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:

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