GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  300 bits (768), Expect = 8e-86
 Identities = 182/511 (35%), Positives = 291/511 (56%), Gaps = 13/511 (2%)

Query: 1   MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60
           MS  +   +I K FPG+ A D V+  V  G++H L+GENGAGKSTL+ +L G YQP+ G 
Sbjct: 1   MSYVIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGE 60

Query: 61  VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRF 120
           +++ G  V+ T    +   GI ++HQ    V   TV EN++LG+ P + G +N ++A + 
Sbjct: 61  ILVKGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKA 120

Query: 121 VRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLF 180
           V    +  G+A+DP AK++ +S+  +Q VEI K L R A ++  DEPT++L+ +E   L 
Sbjct: 121 VETISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELI 180

Query: 181 KLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGR 240
           ++++ L ++ +++I I+H++ EI E+CD CT+ R GR I +    E  T D++ + MVGR
Sbjct: 181 QIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISES-TPDSLAAMMVGR 239

Query: 241 EIS-DIYNYSARPLGEV----RFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSEL 295
           E++  +    A+P   V        K             EV  GEI+G  G+ G G++EL
Sbjct: 240 EVNFSVEKDPAQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTEL 299

Query: 296 MHLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINIS 355
           +  + G     GG + L+G+ I   +  +    G+   P+DR + G+V   TV ENI + 
Sbjct: 300 IEAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQ 359

Query: 356 C--RRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWL-A 412
              ++ Y   G+ L+  +  + A+  I+   ++TPS     R LSGGNQQKAI++R +  
Sbjct: 360 TYYQKPYSTSGV-LNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDR 418

Query: 413 EPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQ 472
            PDL  +I  +PTRG+DVGA   I++ + +  ++G A+++IS EL EVL VSDRI V+ +
Sbjct: 419 SPDL--LIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYE 476

Query: 473 GRISGELTRKDATEQSVLSLALPQSSTALPG 503
           G+I   +   D T ++ L L +   S    G
Sbjct: 477 GKIVA-IVDADKTNENELGLLMAGGSAKKEG 506


Lambda     K      H
   0.320    0.136    0.385 

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: 608
Number of extensions: 35
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 512
Length of database: 509
Length adjustment: 35
Effective length of query: 477
Effective length of database: 474
Effective search space:   226098
Effective search space used:   226098
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