GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05250 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:D8J111
         (520 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  327 bits (839), Expect = 5e-94
 Identities = 191/503 (37%), Positives = 293/503 (58%), Gaps = 11/503 (2%)

Query: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81
           VI ++++ K FPG++A DN   ++  GE+HAL+GENGAGKSTLM +L G+YQ + G+IL+
Sbjct: 4   VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63

Query: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141
            GKPV+IT+P  A  LGIG++HQ   L+   +  +NI +G+EP    G  I+  +  +  
Sbjct: 64  KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEP--TAGGKINIKKAAKAV 121

Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201
             I  +  L +DP   + +++V  QQ VEI K L   + +LI DEPTAAL   EI EL +
Sbjct: 122 ETISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQ 181

Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261
           I++ L ++G  I+ I+HK+ E+ ++ DR +V+R G+ I TV + E++ D++ +MMVGR +
Sbjct: 182 IMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREV 241

Query: 262 DGEQRIPPDTSRNDVVLEVRGL-----NRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVA 316
           +      P     D VL+++ L         A+ D+   +  GEILG AG+ G G+TE+ 
Sbjct: 242 NFSVEKDP-AQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELI 300

Query: 317 RAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSS 376
            AI G      G I ++G      +P      G+G++ +DR   GL +   V  NI L +
Sbjct: 301 EAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQT 360

Query: 377 MGR--FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDC 434
             +  ++  G ++   I + A   +    ++TPS    AR LSGGNQQK +IA+ + R  
Sbjct: 361 YYQKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSP 420

Query: 435 DILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRIT 494
           D+L   +PTRG+DVGA   I+  L    ++GKA+++IS EL EVL +S R+ V+ EG+I 
Sbjct: 421 DLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIV 480

Query: 495 GELARADATQEKIMQLATQRESA 517
             +  AD T E  + L     SA
Sbjct: 481 A-IVDADKTNENELGLLMAGGSA 502


Lambda     K      H
   0.320    0.135    0.372 

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: 607
Number of extensions: 35
Number of successful extensions: 8
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: 520
Length of database: 509
Length adjustment: 35
Effective length of query: 485
Effective length of database: 474
Effective search space:   229890
Effective search space used:   229890
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