GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Alkalihalobacterium alkalinitrilicum DSM 22532

Align RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  630 bits (1625), Expect = 0.0
 Identities = 315/503 (62%), Positives = 398/503 (79%)

Query: 4   HVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIK 63
           +VIEM++I K+F   VAND++ L +++GEIHALLGENGAGKSTLMN+L GL +P  G I 
Sbjct: 3   YVIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEIL 62

Query: 64  INGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIK 123
           + G  V I  P+ + +LGIGMVHQHFMLVE FTVTENIILG E    G +++KKA + ++
Sbjct: 63  VKGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVE 122

Query: 124 ALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTI 183
            +S++YGLAVDP AKI DISVG QQRVEILKTLYRGA+ILIFDEPTA LTP EI EL+ I
Sbjct: 123 TISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQI 182

Query: 184 MKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSVS 243
           MK LV EGKSIILITHKL EI  V DR TVIRRG+ I TV++S +T   LA MMVGR V+
Sbjct: 183 MKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVN 242

Query: 244 FTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQA 303
           F++EK P +PK+ +L IKDLVV ++R I A+  L LEV AGEI+G+AG+DGNGQ+EL++A
Sbjct: 243 FSVEKDPAQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEA 302

Query: 304 ITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYY 363
           ITGLRK   G++ + GQD+T L+ RKIT   VGH+P+DRH+ GL+L+ T+ EN+ LQTYY
Sbjct: 303 ITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYY 362

Query: 364 KAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDL 423
           + P S +GVLN+++I +    L++++DVR  +E   A+  SGGNQQKAIIAREVDR PDL
Sbjct: 363 QKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDL 422

Query: 424 LIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGI 483
           LI +QPTRGLDVGAIE IH RL+ ERD+GKAVLL+S ELDE+LN+SDRIAVI++G+I  I
Sbjct: 423 LIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAI 482

Query: 484 VTPETTNKQELGILMAGGSIERE 506
           V  + TN+ ELG+LMAGGS ++E
Sbjct: 483 VDADKTNENELGLLMAGGSAKKE 505



 Score =  115 bits (289), Expect = 3e-30
 Identities = 81/258 (31%), Positives = 141/258 (54%), Gaps = 17/258 (6%)

Query: 5   VIEMRE-ITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIK 63
           V+++++ + K   D  A + ++L++  GEI  + G +G G++ L+  + GL +PT G+I+
Sbjct: 256 VLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQ 315

Query: 64  INGSAVTIDSPSKSAQLGIGMV----HQHFMLVEAFTVTENIILGNEVVK----NGILDL 115
           +NG  +T  +P K    G+G +    H+H ++++ FTV ENI+L     K    +G+L+ 
Sbjct: 316 LNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLD-FTVGENIVLQTYYQKPYSTSGVLNF 374

Query: 116 KKAGQEIKALSEKYGLAVDPNAKIAD-ISVGAQQRVEILKTLYRGADILIFDEPTAVLTP 174
            +  ++   L E Y +       +A  +S G QQ+  I + + R  D+LI  +PT  L  
Sbjct: 375 NEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDV 434

Query: 175 SEIQELMTIMKSLVKE---GKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQ 231
             I+   +I   LVKE   GK+++LI+ +LDE+ +V+DR+ VI  GK +  V+   T   
Sbjct: 435 GAIE---SIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNEN 491

Query: 232 DLAEMMVGRSVSFTIEKT 249
           +L  +M G S     E T
Sbjct: 492 ELGLLMAGGSAKKEGETT 509


Lambda     K      H
   0.315    0.135    0.363 

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: 774
Number of extensions: 30
Number of successful extensions: 6
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: 510
Length of database: 509
Length adjustment: 34
Effective length of query: 476
Effective length of database: 475
Effective search space:   226100
Effective search space used:   226100
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: 42 (22.0 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