Alignments for a candidate for malK_Ss in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for malK_Ss in Marinobacter adhaerens HP15

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate GFF2860 HP15_2804 oligopeptide/dipeptide ABC transporter, ATP-binding protein-like protein

Query= TCDB::Q97UG5
         (617 letters)



>FitnessBrowser__Marino:GFF2860
          Length = 672

 Score =  345 bits (885), Expect = 4e-99
 Identities = 216/626 (34%), Positives = 344/626 (54%), Gaps = 31/626 (4%)

Query: 5   MDSLLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKY 64
           M S+L + +L+         +  V  ++ E+   E   I GESG GKS  A+A+  LL  
Sbjct: 3   MASILDIQDLSVDIPTDSSTLHAVRGISLELNRGETLGIVGESGSGKSMTALALMNLLPP 62

Query: 65  PGVVLRGHVYLKDKDILSITQEELR-KLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVS 123
                   +     D+   T+ EL  K+R +    + Q  M +L+PV  IG Q+      
Sbjct: 63  AAKRQASCIDFDGSDLTHATERELASKIRGQRIGMIFQEPMTSLNPVYSIGRQLKETMTL 122

Query: 124 H----GVNVEEARKLIKEKLELVDLPYNVVNMYPHELSGGMRQRVVIATSILLNPSLIIL 179
           H        E     + EK+ L D P + +  YPHELSGG RQRV+IA +++  P L+I 
Sbjct: 123 HRKVSDTEAENRAVYLLEKVGLPD-PASRLKQYPHELSGGQRQRVMIAMALMNEPELLIA 181

Query: 180 DEPTTGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGS 239
           DEPTT LDV +Q +IL  L+ +Q++ G+S+++I+HD+ ++   +D + +MYAG+IVE G 
Sbjct: 182 DEPTTALDVTIQAQILHLLRELQQEFGMSMILITHDLGVVSRAADNIAVMYAGDIVETGK 241

Query: 240 KEEIIKRPSHPYTYLLISSLPSLV-KRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKME 298
             E+++ P HPYT  L+  +P    + +++L +IPG  P M   + + C F  RCP    
Sbjct: 242 TGEVLENPRHPYTKGLLECVPGYKGQSQQRLGAIPGIVPAMTGDI-SGCAFASRCPRAAG 300

Query: 299 KCSTLNPALGDIMDGHKARCFLQKGGYVDLSTLPIPLEYYAEEKAETDLSESNQHEVVMK 358
            C T NP    +   H+ R F+     V+   L       +E    T  S     E ++ 
Sbjct: 301 VCRTTNPPTKKL---HQGRYFVCHEPDVEGRGLAAERPTASE---RTVTSNVRGTEDILT 354

Query: 359 ILNLSKIYYIRKNLI-LSEPINAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ 417
           + ++S  + +R+ +    +P+ A++DVS  LKKG + ALVG SG GK+T+ + + G+   
Sbjct: 355 VDHVSCTFSVRRGMFGKRKPLQALDDVSLTLKKGEVLALVGESGCGKTTLTRTIMGLQAP 414

Query: 418 TSGKIILLGKDVSEYGVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSN 477
           ++G + L G+ +        M     +Q IFQDPYSSL+PR T+   + +PL +H   SN
Sbjct: 415 STGSVTLNGQRIENL---PPMDRARMIQPIFQDPYSSLNPRKTIGEIIAKPLFVHGIGSN 471

Query: 478 KDQLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSM 537
           ++Q   ++ ++++ VGL  P +    YP +LSGG+RQR AI RA  + P+V++ DEP S 
Sbjct: 472 QEQ-HQQVRKMMELVGL--PSRVFNSYPDQLSGGQRQRAAIGRALILNPEVVICDEPTSA 528

Query: 538 LDASLRAGILNLIKKFKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVIS 596
           LD S++A ILNL+   +    ++ L++TH+++ V ++AD + V+Y G IVE G   +V+S
Sbjct: 529 LDVSVQAQILNLLLDLRDELDLTYLFVTHNLSVVQHMADRVAVMYLGEIVECGERDQVMS 588

Query: 597 NPSHEYTKRLI---------EAVPDP 613
           +P H YT  L+         E+VPDP
Sbjct: 589 DPKHPYTHALMNSALSISPGESVPDP 614



 Score =  166 bits (420), Expect = 3e-45
 Identities = 100/309 (32%), Positives = 178/309 (57%), Gaps = 20/309 (6%)

Query: 17  GYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVVLRGHVYLK 76
           G F +   +  + +V+  +   E+ A+ GESGCGK+TL   I GL + P     G V L 
Sbjct: 367 GMFGKRKPLQALDDVSLTLKKGEVLALVGESGCGKTTLTRTIMGL-QAPST---GSVTLN 422

Query: 77  DKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSHGVNV-EEARKLI 135
            + I ++   +  + RM + ++   ++  +L+P   IG+ + +    HG+   +E  + +
Sbjct: 423 GQRIENLPPMD--RARMIQPIFQDPYS--SLNPRKTIGEIIAKPLFVHGIGSNQEQHQQV 478

Query: 136 KEKLELVDLPYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTTGLDVIVQYEIL 195
           ++ +ELV LP  V N YP +LSGG RQR  I  +++LNP ++I DEPT+ LDV VQ +IL
Sbjct: 479 RKMMELVGLPSRVFNSYPDQLSGGQRQRAAIGRALILNPEVVICDEPTSALDVSVQAQIL 538

Query: 196 KDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIKRPSHPYTYLL 255
             L  ++ +L ++ + ++H++S++  ++DRV +MY GEIVE G +++++  P HPYT+ L
Sbjct: 539 NLLLDLRDELDLTYLFVTHNLSVVQHMADRVAVMYLGEIVECGERDQVMSDPKHPYTHAL 598

Query: 256 ISSLPSLVKRREKLLSIP-----GNPPLMLSKVPNSCRFYDRCPFKMEKCSTLNPALGDI 310
           ++S  S+        S+P     G+ P  +++ P+ C F+ RCP   ++C    P   ++
Sbjct: 599 MNSALSISPGE----SVPDPGLSGDFPNPMNR-PSGCPFHPRCPLADQQCREQAPG-PEL 652

Query: 311 MDGHKARCF 319
           +D    +C+
Sbjct: 653 IDNTLVQCW 661


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: 997
Number of extensions: 50
Number of successful extensions: 15
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: 672
Length adjustment: 38
Effective length of query: 579
Effective length of database: 634
Effective search space:   367086
Effective search space used:   367086
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 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