GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Alkalihalobacterium alkalinitrilicum DSM 22532

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  276 bits (705), Expect = 2e-78
 Identities = 162/489 (33%), Positives = 269/489 (55%), Gaps = 7/489 (1%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           +  + I K FPG+ A  +++     G++HAL+GENGAGKSTL+ +L G Y P  G +++ 
Sbjct: 5   IEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILVK 64

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127
           G+ +  +D   A   G+ +++Q   LV + TV ENI LG+ P  GG +N           
Sbjct: 65  GKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVETI 124

Query: 128 LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIR 187
            K  G+ +DP   ++ +S+G  Q VEI K L R A+I+ FDEPT++L+ +EI  L ++++
Sbjct: 125 SKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQIMK 184

Query: 188 ELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGD 247
           +L  EG+ I+ ++H+++EI  + D  TV + GR + T  D+ +   D+L   MVGR++  
Sbjct: 185 KLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGT-VDISESTPDSLAAMMVGREVNF 243

Query: 248 IYGWQPRSYGEERLRLDAVKAPGVR-----TPISLAVRSGEIVGLFGLVGAGRSELMKGM 302
                P    +  L++  +     R       + L V +GEI+G+ G+ G G++EL++ +
Sbjct: 244 SVEKDPAQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAI 303

Query: 303 FGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISA-RR 361
            G  + T G + ++ Q I    P     AG+   P+DR   G++   +V +NI +    +
Sbjct: 304 TGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQ 363

Query: 362 KHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVI 421
           K      V+N       A+  I   +++TP    L   LSGGNQQKAI+ R +     ++
Sbjct: 364 KPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLL 423

Query: 422 LLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGEL 481
           +  +PTRG+DVGA   I++ +     +G AVL  S +L EVL V+DRI V+ EG+I   +
Sbjct: 424 IAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIV 483

Query: 482 LHEQADERQ 490
             ++ +E +
Sbjct: 484 DADKTNENE 492


Lambda     K      H
   0.319    0.136    0.391 

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: 659
Number of extensions: 36
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: 504
Length of database: 509
Length adjustment: 34
Effective length of query: 470
Effective length of database: 475
Effective search space:   223250
Effective search space used:   223250
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 (21.7 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