Alignments for a candidate for malK_Ss in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for malK_Ss in Halomonas desiderata SP1

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate WP_086508118.1 BZY95_RS00870 ABC transporter ATP-binding protein

Query= TCDB::Q97UG5
         (617 letters)



>NCBI__GCF_002151265.1:WP_086508118.1
          Length = 766

 Score =  451 bits (1160), Expect = e-131
 Identities = 246/623 (39%), Positives = 378/623 (60%), Gaps = 19/623 (3%)

Query: 8   LLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGV 67
           LLKV +L   Y    G V  V  ++F++ P E   + GESGCGK+T A A+  LL   G 
Sbjct: 6   LLKVEDLAIHYRTGAGPVQAVDGIHFDLRPGEALGLVGESGCGKTTAAKAMLRLLPPNGE 65

Query: 68  VLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-GV 126
           V RG +    +D++++ +E +RK+R KE  ++ Q AM+ALDPV  +GDQ++ A  +H  +
Sbjct: 66  VPRGRIDFDGRDLVALDEESMRKVRWKEIAWISQAAMNALDPVYTVGDQILEAMNAHIKI 125

Query: 127 NVEEARKLIKEKLELVDLPYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTTGL 186
           + + A    +E    V +    ++ YPHE+SGGM+QR VIA ++ L+P LII DEPTT L
Sbjct: 126 DRKTAWAHAEELFRAVGIDPGRLSAYPHEMSGGMKQRAVIAMALALDPKLIIADEPTTAL 185

Query: 187 DVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIKR 246
           DV+ Q +IL  L +++R+ G+ L+ I+HDIS+++   DRV +MY G I+E G   E+   
Sbjct: 186 DVVTQAQILARLSKLRRERGMGLLFITHDISVVVQTCDRVAVMYGGHIMETGPVREVFGT 245

Query: 247 PSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLNPA 306
           P HPYT  L ++ P+L   + +L+SIPG+PP +L+  P+ CRF +RCPF  E+C    P 
Sbjct: 246 PFHPYTMGLTNAFPTLEGAQRELISIPGSPPDLLNP-PSGCRFAERCPFATERCVRETPP 304

Query: 307 LGDIMDGHKARCFL--QKGGYVDLSTLPIPLEYYAEEKAE-TDLSESNQH-----EVVMK 358
           L  + +  +A C    Q   +   + L        E   E    + S +H      ++++
Sbjct: 305 LHPVGEERQAACHYPDQAEAFRVKAALNETWAVVGERLNEPVQGAGSIEHLETEAPLLLE 364

Query: 359 ILNLSKIYYIRKNLI-------LSEPINAVNDVSFELKKGTITALVGGSGHGKSTIAKIL 411
           +  L K + + +  +           ++AV+ +SF+L++G I  L G SG GK+T  ++L
Sbjct: 365 VEELKKHFPVEQGFLDGLRGRNKDRKVHAVDGISFDLREGEILGLAGESGSGKTTTGEML 424

Query: 412 AGMIQQTSGKIILLGKDVSEYGVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLI 471
             ++  T G+I   G D+++   R    ++   QMIFQDPY +L+PR T+   V  PL+I
Sbjct: 425 VRLLDVTEGEIRFEGADIAQLTGRELKTFRRRAQMIFQDPYQTLNPRFTIFDIVAEPLII 484

Query: 472 HKKVSNKDQLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVA 531
           H +++  + L  K++  L+  GLKP E Y  ++PHELSGG+RQRVAIARA  +EP+ +VA
Sbjct: 485 H-RLAEGEALRQKVVVALERAGLKPAEVYAERFPHELSGGQRQRVAIARAIVLEPRFIVA 543

Query: 532 DEPVSMLDASLRAGILNLIKKFKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGN 590
           DEPVSMLD S+RAG+LNL+ +F+   GIS +Y++HD+ T+ Y+AD   ++Y G IVE G 
Sbjct: 544 DEPVSMLDVSIRAGVLNLMHRFRNELGISFVYVSHDLPTIRYVADRTAIMYLGEIVEVGP 603

Query: 591 TYEVISNPSHEYTKRLIEAVPDP 613
           T +V+    H YT+ L+EA P+P
Sbjct: 604 TEQVVRERKHPYTQLLLEASPEP 626



 Score =  160 bits (406), Expect = 1e-43
 Identities = 104/288 (36%), Positives = 154/288 (53%), Gaps = 16/288 (5%)

Query: 20  NQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVVLRGHVYLKDKD 79
           N+D  V  V  ++F++   EI  +AGESG GK+T    +  LL     V  G +  +  D
Sbjct: 386 NKDRKVHAVDGISFDLREGEILGLAGESGSGKTTTGEMLVRLLD----VTEGEIRFEGAD 441

Query: 80  ILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSHGVNVEEA-RKLIKEK 138
           I  +T  EL+  R +  + + Q     L+P   I D +    + H +   EA R+ +   
Sbjct: 442 IAQLTGRELKTFRRRAQM-IFQDPYQTLNPRFTIFDIVAEPLIIHRLAEGEALRQKVVVA 500

Query: 139 LELVDL-PYNV-VNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTTGLDVIVQYEILK 196
           LE   L P  V    +PHELSGG RQRV IA +I+L P  I+ DEP + LDV ++  +L 
Sbjct: 501 LERAGLKPAEVYAERFPHELSGGQRQRVAIARAIVLEPRFIVADEPVSMLDVSIRAGVLN 560

Query: 197 DLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIKRPSHPYTYLLI 256
            + R + +LG+S V +SHD+  +  ++DR  IMY GEIVE+G  E++++   HPYT LL+
Sbjct: 561 LMHRFRNELGISFVYVSHDLPTIRYVADRTAIMYLGEIVEVGPTEQVVRERKHPYTQLLL 620

Query: 257 SSL----PSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKC 300
            +     P++VK     L   G  P  + + PN C F+ RCP  M  C
Sbjct: 621 EASPEPDPAVVK---PPLESAGEIPSAV-EPPNGCHFHTRCPRAMAHC 664


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: 1092
Number of extensions: 48
Number of successful extensions: 13
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 4
Length of query: 617
Length of database: 766
Length adjustment: 39
Effective length of query: 578
Effective length of database: 727
Effective search space:   420206
Effective search space used:   420206
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 24 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