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_092483976.1 BM299_RS11015 ABC transporter ATP-binding protein

Query= TCDB::Q97UG5
         (617 letters)



>NCBI__GCF_900115975.1:WP_092483976.1
          Length = 319

 Score =  204 bits (518), Expect = 6e-57
 Identities = 115/315 (36%), Positives = 177/315 (56%), Gaps = 4/315 (1%)

Query: 8   LLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGV 67
           LL + +L+  +    G V  +  V+  V   EI AI GESG GKS  A++I GLL     
Sbjct: 2   LLDIKQLSVSFQTFQGSVHVLDRVSLSVDRGEILAIVGESGSGKSVTALSILGLLDKNAK 61

Query: 68  VLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSHG-V 126
           + +G++     D+  ++ +E++K R K    V Q  M AL P  +IGDQ+      H  +
Sbjct: 62  IEQGNIVFDGTDLTKLSTKEIQKYRGKRIGMVFQEPMTALHPTMRIGDQLTNVIKRHHKL 121

Query: 127 NVEEARKLIKEKLELVDL--PYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTT 184
             +E+  ++ E L+ V    P  +   YPHELSGGMRQR+VIA ++   P L+I DEPTT
Sbjct: 122 TKKESHPIMLEMLKDVHFEEPELIAQKYPHELSGGMRQRIVIALAMSAPPELLIADEPTT 181

Query: 185 GLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEII 244
            LDV +Q EIL  +K + ++  +++++I+HD+ ++  +SD V +MYAG+I+E G+ +EI+
Sbjct: 182 ALDVTIQAEILTLMKELTQKYNIAVILITHDLGVVREVSDNVCVMYAGKILEKGTTKEIL 241

Query: 245 KRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLN 304
             P HPYT LL+ +LP  V   E+L  I G  P +   +P  C F  RCP   ++C    
Sbjct: 242 DNPKHPYTNLLLRALPDQVNPGERLQEIEGEVPDLKQHLP-GCIFSSRCPLSKDECFIKA 300

Query: 305 PALGDIMDGHKARCF 319
           P    + +     C+
Sbjct: 301 PPQLSLSETQMVHCW 315



 Score =  172 bits (437), Expect = 1e-47
 Identities = 89/241 (36%), Positives = 150/241 (62%), Gaps = 7/241 (2%)

Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQTS----GKIILLGKDVSEYG 433
           ++ ++ VS  + +G I A+VG SG GKS  A  + G++ + +    G I+  G D+++  
Sbjct: 19  VHVLDRVSLSVDRGEILAIVGESGSGKSVTALSILGLLDKNAKIEQGNIVFDGTDLTKLS 78

Query: 434 VRNSMWYK-ENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKNV 492
            +    Y+ + + M+FQ+P ++L P   +   +   +  H K++ K+   P ++E+LK+V
Sbjct: 79  TKEIQKYRGKRIGMVFQEPMTALHPTMRIGDQLTNVIKRHHKLTKKESH-PIMLEMLKDV 137

Query: 493 GLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKK 552
             + PE    KYPHELSGG RQR+ IA A +  P++L+ADEP + LD +++A IL L+K+
Sbjct: 138 HFEEPELIAQKYPHELSGGMRQRIVIALAMSAPPELLIADEPTTALDVTIQAEILTLMKE 197

Query: 553 F-KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611
             +K  I+++ ITHD+  V  ++D + V+Y G+I+EKG T E++ NP H YT  L+ A+P
Sbjct: 198 LTQKYNIAVILITHDLGVVREVSDNVCVMYAGKILEKGTTKEILDNPKHPYTNLLLRALP 257

Query: 612 D 612
           D
Sbjct: 258 D 258


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: 504
Number of extensions: 25
Number of successful extensions: 7
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: 319
Length adjustment: 32
Effective length of query: 585
Effective length of database: 287
Effective search space:   167895
Effective search space used:   167895
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