Alignments for a candidate for malK_Ss in Halococcus hamelinensis 100A6

GapMind for catabolism of small carbon sources

Alignments for a candidate for malK_Ss in Halococcus hamelinensis 100A6

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate WP_007691333.1 C447_RS04485 ABC transporter ATP-binding protein

Query= TCDB::Q97UG5
         (617 letters)



>NCBI__GCF_000336675.1:WP_007691333.1
          Length = 520

 Score =  240 bits (612), Expect = 1e-67
 Identities = 167/531 (31%), Positives = 260/531 (48%), Gaps = 79/531 (14%)

Query: 5   MDSLLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKY 64
           M  LL ++ L   +    G V  V  ++  V   E   + GESG GKS  A++  GL+  
Sbjct: 1   MTDLLSLSGLRTQFATDRGTVKAVDGLDLTVEKGETVGLVGESGSGKSVTALSTMGLVDS 60

Query: 65  PGVVLRGHVYLKDKDILSITQEE----------------------LRKLRMKEFVYVPQF 102
           PG V+ G V   D D+     EE                      +R++R  E   + Q 
Sbjct: 61  PGRVVDGSVEFHDADLARTFAEEYRGDFADPERGTVDLTRAPDDAMRRVRGGEMSMIFQD 120

Query: 103 AMDALDPVAKIGDQMMRAAVSH---------------------GVNVEEARKLIKEKLEL 141
            M +L+P   +G+Q+  +   H                     G  +++  +++++ +E+
Sbjct: 121 PMTSLNPAVPVGEQVAESLRLHQYGGRRKDSWFNAVREVVPRVGSGLDD--RVLEDTIEM 178

Query: 142 VDL-----PYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTTGLDVIVQYEILK 196
           +       P   V  +PHE SGGMRQRV+IA ++   P L+I DEPTT LDV +Q +IL 
Sbjct: 179 LSAVGIPEPAARVEEFPHEFSGGMRQRVLIAIALACRPQLLIADEPTTALDVTIQAQILD 238

Query: 197 DLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIKRPSHPYTYLLI 256
            +  +Q + G+S++ I+HD+ ++    DRV +MYAGEIVE G  EEI   PSHPYTY L+
Sbjct: 239 LINDLQDEFGMSVLFITHDLGVVAETCDRVAVMYAGEIVEEGPVEEIFANPSHPYTYTLL 298

Query: 257 SSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCST-----LNPALGDIM 311
            S+P   +  ++L  I GN P ++  +P  CRF  RCP+   +C       L     D+ 
Sbjct: 299 ESIPR--EDADRLTPIEGNVPDLID-LPEGCRFAPRCPWAHAECREDPIPYLQHGPEDV- 354

Query: 312 DGHKARCFLQKGGYVDLSTLPIPLEYYAEEKA----ETDLSESNQHEVVMKILNLSKIYY 367
             H+++C LQ+    D S      EY  +E      E   +     E ++ +  + K + 
Sbjct: 355 -NHRSKCVLQE---FDTS------EYGTDEGVAATDEPTAAPDRTGEPLVSVEGMKKHFS 404

Query: 368 IRKNLILS------EPINAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQTSGK 421
             + L+ S      +P+ AV+ V F++ +G    LVG SG GKST  + +  +++ T GK
Sbjct: 405 QTEGLLDSWLASDTKPVRAVDGVDFDVYEGETLGLVGESGCGKSTTGRTVLRLLEPTDGK 464

Query: 422 IILLGKDVSEYGVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIH 472
           ++  G+D++          +  +QMIFQDP SSLDPR  V   +  PL IH
Sbjct: 465 VVFAGEDLAGLDGDALREKRREMQMIFQDPLSSLDPRMNVGATIAEPLTIH 515



 Score =  139 bits (349), Expect = 4e-37
 Identities = 92/282 (32%), Positives = 139/282 (49%), Gaps = 48/282 (17%)

Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ----TSGKIILLGKDVS--- 430
           + AV+ +   ++KG    LVG SG GKS  A    G++        G +     D++   
Sbjct: 21  VKAVDGLDLTVEKGETVGLVGESGSGKSVTALSTMGLVDSPGRVVDGSVEFHDADLARTF 80

Query: 431 -----------EYGVRNSMWYKEN---------VQMIFQDPYSSLDPRHTVRWHVERPLL 470
                      E G  +     ++         + MIFQDP +SL+P   V   V   L 
Sbjct: 81  AEEYRGDFADPERGTVDLTRAPDDAMRRVRGGEMSMIFQDPMTSLNPAVPVGEQVAESLR 140

Query: 471 IHKKVSNK--------------------DQLLPKIIEVLKNVGLKPPEKYLYKYPHELSG 510
           +H+    +                    D++L   IE+L  VG+  P   + ++PHE SG
Sbjct: 141 LHQYGGRRKDSWFNAVREVVPRVGSGLDDRVLEDTIEMLSAVGIPEPAARVEEFPHEFSG 200

Query: 511 GERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKKFKKN-GISILYITHDIAT 569
           G RQRV IA A A  P++L+ADEP + LD +++A IL+LI   +   G+S+L+ITHD+  
Sbjct: 201 GMRQRVLIAIALACRPQLLIADEPTTALDVTIQAQILDLINDLQDEFGMSVLFITHDLGV 260

Query: 570 VNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611
           V    D + V+Y G IVE+G   E+ +NPSH YT  L+E++P
Sbjct: 261 VAETCDRVAVMYAGEIVEEGPVEEIFANPSHPYTYTLLESIP 302


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: 773
Number of extensions: 38
Number of successful extensions: 11
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: 520
Length adjustment: 36
Effective length of query: 581
Effective length of database: 484
Effective search space:   281204
Effective search space used:   281204
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources