GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfR in Alkalihalobacterium alkalinitrilicum DSM 22532

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  278 bits (712), Expect = 2e-79
 Identities = 166/479 (34%), Positives = 264/479 (55%), Gaps = 6/479 (1%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           ++  + + K FPG+ A DNV   +++GEI ALLGENGAGKSTL+  L G+Y  ++G I +
Sbjct: 4   VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128
           +G+ +   +   A +LGIG V+Q   L+   +V +N+ +G+EP   G +  K+  K    
Sbjct: 64  KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVET 123

Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
           +   YG ++D    +   SV MQQ V I + +   A++LI DEPTA+L  QE+  L  +M
Sbjct: 124 ISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQIM 183

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDT 248
           ++L   G S+I +TH L ++ +V DR TV+R G  +G  +  E     L  MM+GRE++ 
Sbjct: 184 KKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVNF 243

Query: 249 HALQRAGR---TLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEV 305
              +   +    +L  K +   K+      +    LEV  GEI+G+AG+ G+G+TE  E 
Sbjct: 244 SVEKDPAQPKDAVLQIKDLVV-KDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEA 302

Query: 306 IFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQA 365
           I G++    G   + G+     +P + +  G+G  P+DR   G++   +V ENI+L    
Sbjct: 303 ITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYY 362

Query: 366 QRGWLRP--ISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQF 423
           Q+ +     ++  E  + A   I    +RTPS       LSGGNQQK +++R +   P  
Sbjct: 363 QKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDL 422

Query: 424 LILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVA 482
           LI  +PTRG+DVGA   I   +      G A+L+IS EL+E++  +DR+ ++ + K VA
Sbjct: 423 LIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVA 481



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 60/208 (28%), Positives = 113/208 (54%), Gaps = 6/208 (2%)

Query: 281 LEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFC 340
           L+V+ GEI  L G  G+G++    V+FG+   + G  L+KGKP  +  P+ A+ LGIG  
Sbjct: 25  LQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILVKGKPVKITDPNVANRLGIGMV 84

Query: 341 PEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPI 400
            +      ++   +V ENIIL  +   G    I+ K+  +  E   +Q G+      + I
Sbjct: 85  HQHFM---LVEKFTVTENIILGKEPTAGG--KINIKKAAKAVETISKQYGLAVDPYAK-I 138

Query: 401 EFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISS 460
           + +S G QQ+V + + L    + LI DEPT  +      E+I++++ L ++G ++++I+ 
Sbjct: 139 QDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQIMKKLVSEGKSIILITH 198

Query: 461 ELEELVGYADRVIIMRDRKQVAEIPLAE 488
           +L+E++   DR  ++R  + +  + ++E
Sbjct: 199 KLKEIMEVCDRCTVIRRGRGIGTVDISE 226



 Score = 94.4 bits (233), Expect = 9e-24
 Identities = 68/234 (29%), Positives = 117/234 (50%), Gaps = 16/234 (6%)

Query: 22  VKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHA 81
           + A++++   +  GEI+ + G +G G++ LI+A+TG+     G I L GQ I+       
Sbjct: 270 ITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQLNGQDITGLTPRKI 329

Query: 82  QQLGIGTVYQEVN---LLPNMSVADNL----FIGREPKRFGLLRRKEMEKRATELMASYG 134
              G+G + Q+ +   L+ + +V +N+    +  +     G+L   E+ K+A EL+  Y 
Sbjct: 330 TGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVLNFNEIYKKANELIEDY- 388

Query: 135 FSLDVREPLNR-----FSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMR 189
              DVR P         S   QQ   I R +D S  +LI  +PT  LD   +E +   + 
Sbjct: 389 ---DVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDVGAIESIHHRLV 445

Query: 190 QLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243
           + RD+G +++ ++  LD+V  VSDRI V+  G  V   +  +  + EL  +M G
Sbjct: 446 KERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENELGLLMAG 499


Lambda     K      H
   0.321    0.138    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: 585
Number of extensions: 26
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 500
Length of database: 509
Length adjustment: 34
Effective length of query: 466
Effective length of database: 475
Effective search space:   221350
Effective search space used:   221350
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