GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  277 bits (709), Expect = 6e-79
 Identities = 174/496 (35%), Positives = 273/496 (55%), Gaps = 21/496 (4%)

Query: 7   IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66
           ++ MK I  EFPG+ A D V L +  GE+HAL+GENGAGKST++  L G+Y+   G I+V
Sbjct: 4   VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63

Query: 67  DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKK 126
            GKP +      A   GI  V+Q   L    +V EN++LG E      I+ KK  +A + 
Sbjct: 64  KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVET 123

Query: 127 YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAI 186
              Q GL ++DP+  +  IS+ MQQ V I + +   A++LI DEPT++L   E+ +L  I
Sbjct: 124 ISKQYGL-AVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQI 182

Query: 187 MRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKS-- 244
           M+K+   G +I+ ++H L +I E+ DR T++R G+ I  V   ++  D L  MM+G+   
Sbjct: 183 MKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVN 242

Query: 245 -AAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303
            + E      K A  +I    K +V VK       +N + ++++ GE++G AG+ G+G+T
Sbjct: 243 FSVEKDPAQPKDAVLQI----KDLV-VKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQT 297

Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363
           EL   + G  KP  G   LNG+ +    P       + +  ++R   G++ D TV +NI+
Sbjct: 298 ELIEAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIV 357

Query: 364 IAL-----QATRGM--FKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLI 416
           +        +T G+  F  I KK A+ +++ Y    +VR        + LSGGNQQK +I
Sbjct: 358 LQTYYQKPYSTSGVLNFNEIYKK-ANELIEDY----DVRTPSEHTLARALSGGNQQKAII 412

Query: 417 GRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIE 476
            R +   P+LLI  +PTRG+D+GA   I   ++    +G  V+ IS EL+EV+ +SD I 
Sbjct: 413 AREVDRSPDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIA 472

Query: 477 VLKDRHKIAEIENDDT 492
           V+ +   +A ++ D T
Sbjct: 473 VIYEGKIVAIVDADKT 488



 Score = 95.1 bits (235), Expect = 5e-24
 Identities = 62/250 (24%), Positives = 130/250 (52%), Gaps = 8/250 (3%)

Query: 4   KNPIVVMKGITI-EFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAG 62
           K+ ++ +K + + +   + A++ + L ++ GE+  + G +G G++ +I+A+TG+ K   G
Sbjct: 253 KDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGG 312

Query: 63  SIMVDGKPQQFNGTLDAQNAGIATVYQEVN---LCTNLSVGENVMLGHEKRGPFG----I 115
           +I ++G+            AG+  + Q+ +   L  + +VGEN++L    + P+     +
Sbjct: 313 NIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVL 372

Query: 116 DWKKTHEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSL 175
           ++ + ++ A + +    + +   HT   ++S   QQ   IAR +  +  +LI  +PT  L
Sbjct: 373 NFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGL 432

Query: 176 DANEVRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDE 235
           D   +  +   + K RD G A+L +S  LD++  ++DR+ ++  G+ +  V    T  +E
Sbjct: 433 DVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENE 492

Query: 236 LIGMMIGKSA 245
           L  +M G SA
Sbjct: 493 LGLLMAGGSA 502


Lambda     K      H
   0.316    0.135    0.376 

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: 685
Number of extensions: 44
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 513
Length of database: 509
Length adjustment: 35
Effective length of query: 478
Effective length of database: 474
Effective search space:   226572
Effective search space used:   226572
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 (21.6 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