GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Ss in Desulfovibrio vulgaris Miyazaki F

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate 8500263 DvMF_1020 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q97UG5
         (617 letters)



>FitnessBrowser__Miya:8500263
          Length = 358

 Score =  192 bits (488), Expect = 2e-53
 Identities = 104/285 (36%), Positives = 167/285 (58%), Gaps = 6/285 (2%)

Query: 28  VTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVVLRGHVYLKDKDILSITQEE 87
           V  ++F + P     + GESGCGKS  A+A+  L+  PG V  G V L+ +++L++ + E
Sbjct: 44  VAGISFSIAPGGTLCLVGESGCGKSMTALALLRLVPEPGRVASGSVRLEGRELLTLPEPE 103

Query: 88  LRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-GVNVEEARKLIKEKLELVDLPY 146
           +R +R +    + Q  M +L+PV ++G+Q+      H G++  +A     + L  V +P 
Sbjct: 104 MRGVRGRSISMIFQEPMTSLNPVFRVGEQIAEGVRLHLGLSRSDAAARAVDLLRQVGIPS 163

Query: 147 NVVNM--YPHELSGGMRQRVVIATSILLNPSLIILDEPTTGLDVIVQYEILKDLKRIQRQ 204
             +    +PH++SGGMRQRV+IA ++  +P L+I DEPTT LDV +Q +IL+ ++ +   
Sbjct: 164 PELRARDFPHQMSGGMRQRVMIAMALACDPRLLIADEPTTALDVTIQRQILRLMRDLAAH 223

Query: 205 LGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIKRPSHPYTYLLISSLPSLVK 264
            G S+++I+HD+ ++   +D V +MYAG I+E  S  +   RP HPY   L+ S+P  V 
Sbjct: 224 RGASVLLITHDLGVVAETADHVAVMYAGRIMEHASVGDFFARPLHPYAQGLMRSVPQAVS 283

Query: 265 --RREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLNPAL 307
             R E+L +IPG  P  L  +P+ C F DRCP    +C+   P L
Sbjct: 284 GPRAERLSAIPGTVP-PLWALPSGCTFRDRCPHAFARCAEQEPPL 327



 Score =  144 bits (362), Expect = 8e-39
 Identities = 86/246 (34%), Positives = 136/246 (55%), Gaps = 17/246 (6%)

Query: 377 PINAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ----TSGKIILLGKDVSEY 432
           P+ AV  +SF +  G    LVG SG GKS  A  L  ++ +     SG + L G+++   
Sbjct: 40  PLRAVAGISFSIAPGGTLCLVGESGCGKSMTALALLRLVPEPGRVASGSVRLEGRELLTL 99

Query: 433 ------GVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKII 486
                 GVR       ++ MIFQ+P +SL+P   V   +   + +H  +S  D    + +
Sbjct: 100 PEPEMRGVRG-----RSISMIFQEPMTSLNPVFRVGEQIAEGVRLHLGLSRSDAAA-RAV 153

Query: 487 EVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGI 546
           ++L+ VG+  PE     +PH++SGG RQRV IA A A +P++L+ADEP + LD +++  I
Sbjct: 154 DLLRQVGIPSPELRARDFPHQMSGGMRQRVMIAMALACDPRLLIADEPTTALDVTIQRQI 213

Query: 547 LNLIKKFKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKR 605
           L L++    + G S+L ITHD+  V   AD + V+Y GRI+E  +  +  + P H Y + 
Sbjct: 214 LRLMRDLAAHRGASVLLITHDLGVVAETADHVAVMYAGRIMEHASVGDFFARPLHPYAQG 273

Query: 606 LIEAVP 611
           L+ +VP
Sbjct: 274 LMRSVP 279


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: 447
Number of extensions: 17
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: 358
Length adjustment: 33
Effective length of query: 584
Effective length of database: 325
Effective search space:   189800
Effective search space used:   189800
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 Sep 17 2021. 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