GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Ss in Desulfoscipio geothermicus DSM 3669

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate WP_092481461.1 BM299_RS19630 ABC transporter ATP-binding protein

Query= TCDB::Q97UG5
         (617 letters)



>NCBI__GCF_900115975.1:WP_092481461.1
          Length = 326

 Score =  214 bits (545), Expect = 4e-60
 Identities = 118/321 (36%), Positives = 188/321 (58%), Gaps = 5/321 (1%)

Query: 8   LLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYP-G 66
           LL V +L   +F  DG V  V  V+F +   E  A+ GESG GKS  +++I  L+  P G
Sbjct: 5   LLNVEDLKTHFFLDDGVVPAVDGVSFHLRKGETLAVVGESGSGKSITSLSIMRLVPAPPG 64

Query: 67  VVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSHG- 125
            ++ G +    +D+L+ +++E+R +R      + Q  M +L+PV ++GDQ+  + V H  
Sbjct: 65  RIVGGRITFAGEDLLAKSEKEMRDVRGNRISMIFQEPMTSLNPVYRVGDQIAESLVLHKR 124

Query: 126 VNVEEARKLIKEKLELVDLPY--NVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPT 183
           +  +EA +   E L L  +P     V  +PH++SGGMRQRV+IA ++   P L+I DEPT
Sbjct: 125 MKKKEALEQAVEMLRLTGIPSPEKRVRDFPHQMSGGMRQRVMIAMALCCQPELLIADEPT 184

Query: 184 TGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEI 243
           T LDV +Q +IL+ ++ +QRQ+  S+++I+HD++++  ++DR  +MY G++VE     E+
Sbjct: 185 TALDVTIQAQILELMQELQRQMNTSIILITHDLAVVAEVADRAVVMYCGKVVEEAPVAEL 244

Query: 244 IKRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTL 303
            + P HPYT  L++S+P L +  ++L  I G  P ML ++P  C F  RCP   E C   
Sbjct: 245 FENPLHPYTRGLLNSIPRLDENVDRLFMIDGVVPNML-RLPPGCAFAPRCPEAREHCRET 303

Query: 304 NPALGDIMDGHKARCFLQKGG 324
            P L  +  G    C L +GG
Sbjct: 304 APRLTRVAPGRLVSCLLVEGG 324



 Score =  163 bits (413), Expect = 9e-45
 Identities = 88/241 (36%), Positives = 148/241 (61%), Gaps = 8/241 (3%)

Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQTSGKII-----LLGKDVSEY 432
           + AV+ VSF L+KG   A+VG SG GKS  +  +  ++    G+I+       G+D+   
Sbjct: 22  VPAVDGVSFHLRKGETLAVVGESGSGKSITSLSIMRLVPAPPGRIVGGRITFAGEDLLAK 81

Query: 433 GVRNSMWYKEN-VQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKN 491
             +     + N + MIFQ+P +SL+P + V   +   L++HK++  K+ L  + +E+L+ 
Sbjct: 82  SEKEMRDVRGNRISMIFQEPMTSLNPVYRVGDQIAESLVLHKRMKKKEAL-EQAVEMLRL 140

Query: 492 VGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIK 551
            G+  PEK +  +PH++SGG RQRV IA A   +P++L+ADEP + LD +++A IL L++
Sbjct: 141 TGIPSPEKRVRDFPHQMSGGMRQRVMIAMALCCQPELLIADEPTTALDVTIQAQILELMQ 200

Query: 552 KFKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAV 610
           + ++    SI+ ITHD+A V  +AD  +V+Y G++VE+    E+  NP H YT+ L+ ++
Sbjct: 201 ELQRQMNTSIILITHDLAVVAEVADRAVVMYCGKVVEEAPVAELFENPLHPYTRGLLNSI 260

Query: 611 P 611
           P
Sbjct: 261 P 261


Lambda     K      H
   0.319    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: 419
Number of extensions: 20
Number of successful extensions: 8
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: 617
Length of database: 326
Length adjustment: 33
Effective length of query: 584
Effective length of database: 293
Effective search space:   171112
Effective search space used:   171112
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: 51 (24.3 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