GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Methanosarcina acetivorans C2A

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_011022097.1 MA_RS10955 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>NCBI__GCF_000007345.1:WP_011022097.1
          Length = 267

 Score =  122 bits (307), Expect = 1e-32
 Identities = 94/272 (34%), Positives = 136/272 (50%), Gaps = 28/272 (10%)

Query: 3   QHVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSI 62
           Q+++ ++ +TKKFDD  A   I+ D+  G I A LG NGAGKST + ML  +L PTSG I
Sbjct: 2   QNILSVKSLTKKFDDLTAVKGISFDVETGSIFAFLGPNGAGKSTTIKMLTTVLRPTSGEI 61

Query: 63  KINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQE- 121
            ING           A+   G+V Q + L    T  EN+   + + K     + KA +E 
Sbjct: 62  LINGYNAL--KEQDKARSSFGIVFQDYSLDSELTAYENMEYHSVIYK-----VPKAEREE 114

Query: 122 -IKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQEL 180
            IK   E  GL    N  +   S G ++R+EI + L     +L  DEPT  L P     +
Sbjct: 115 RIKTALEIVGLWNRRNDLVKKYSGGMKRRLEIARALVHYPKVLFLDEPTVGLDPQTRMSI 174

Query: 181 MTIMKSLVKEGK-SIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVG 239
              +K L +E K +I L TH +DE  ++AD++ +I  GK IE    SGT    LAE+M  
Sbjct: 175 WNHIKRLNEERKMTIFLTTHYMDEAEAMADKIAIIDHGKIIE----SGT----LAEIM-- 224

Query: 240 RSVSFTIEKTPTKP-KETILSIKDLVVNENRG 270
                  E+T T+  +E+ L +    + +  G
Sbjct: 225 -------ERTETESLEESFLKLTGRDIRDENG 249



 Score = 74.7 bits (182), Expect = 4e-18
 Identities = 72/268 (26%), Positives = 123/268 (45%), Gaps = 32/268 (11%)

Query: 255 ETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGH 314
           + ILS+K L    +  + A+KG+S +V+ G I    G +G G+S  ++ +T + +  SG 
Sbjct: 2   QNILSVKSLTKKFD-DLTAVKGISFDVETGSIFAFLGPNGAGKSTTIKMLTTVLRPTSGE 60

Query: 315 LTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQT-YYKAPLSHNGVL 373
           + I G +  K   +     S G V +D   D    ELT  EN+   +  YK P +     
Sbjct: 61  ILINGYNALKEQDK--ARSSFGIVFQDYSLDS---ELTAYENMEYHSVIYKVPKA----- 110

Query: 374 NYSKINEHGRHLMQEFDVRG----ANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQP 429
                 E    +    ++ G     N+L+  K +SGG +++  IAR +   P +L + +P
Sbjct: 111 ------EREERIKTALEIVGLWNRRNDLV--KKYSGGMKRRLEIARALVHYPKVLFLDEP 162

Query: 430 TRGLDVGAIEYIHKRLIAERDEGK-AVLLVSFELDEILNLSDRIAVIHDGQI-------Q 481
           T GLD      I   +    +E K  + L +  +DE   ++D+IA+I  G+I       +
Sbjct: 163 TVGLDPQTRMSIWNHIKRLNEERKMTIFLTTHYMDEAEAMADKIAIIDHGKIIESGTLAE 222

Query: 482 GIVTPETTNKQELGILMAGGSIEREEIN 509
            +   ET + +E  + + G  I  E  N
Sbjct: 223 IMERTETESLEESFLKLTGRDIRDENGN 250


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: 307
Number of extensions: 22
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: 267
Length adjustment: 30
Effective length of query: 480
Effective length of database: 237
Effective search space:   113760
Effective search space used:   113760
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: 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