GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  148 bits (373), Expect = 2e-40
 Identities = 76/237 (32%), Positives = 142/237 (59%), Gaps = 1/237 (0%)

Query: 1   MSDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGD 60
           MS ++E++D+ K F  + A D V++++ +GE+ ALLG+NGAGKSTL+ ++ G ++P++G+
Sbjct: 1   MSYVIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGE 60

Query: 61  LVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEE 120
           ++ +GK V    PN A  LGI  ++Q   L+    +  NI L +E T    +N KK  + 
Sbjct: 61  ILVKGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKA 120

Query: 121 SKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKV 180
            + +     + + D   K++++S G +Q V + + +Y  A++++ DEPTAAL+  E  ++
Sbjct: 121 VETISKQYGLAV-DPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITEL 179

Query: 181 LELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237
           +++ + L  +G  +++ITH + +  EV DR  V+ RG+ I      E+  + +  +M
Sbjct: 180 IQIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMM 236



 Score = 95.1 bits (235), Expect = 2e-24
 Identities = 65/242 (26%), Positives = 122/242 (50%), Gaps = 8/242 (3%)

Query: 4   LLEIRD-VHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLV 62
           +L+I+D V K    + A++ + +E++ GE++ + G +G G++ LI+ I+G  KP  G++ 
Sbjct: 256 VLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQ 315

Query: 63  FEGKKVIFNSPNDARSLGIETIYQDL---ALIPDLPIYYNIFLA----REVTNKIFLNKK 115
             G+ +   +P      G+  I QD     L+ D  +  NI L     +  +    LN  
Sbjct: 316 LNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVLNFN 375

Query: 116 KMMEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVV 175
           ++ +++ +L++   +R P  +     LSGG +Q   +AR V  S  +++  +PT  L V 
Sbjct: 376 EIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDVG 435

Query: 176 EARKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITE 235
               +       + KG  VL+I+  + +   V+DRI V+  GKI+     ++TN  E+  
Sbjct: 436 AIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENELGL 495

Query: 236 VM 237
           +M
Sbjct: 496 LM 497


Lambda     K      H
   0.318    0.137    0.371 

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: 323
Number of extensions: 12
Number of successful extensions: 4
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: 251
Length of database: 509
Length adjustment: 29
Effective length of query: 222
Effective length of database: 480
Effective search space:   106560
Effective search space used:   106560
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: 49 (23.5 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