Alignments for a candidate for malK_Ss in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for malK_Ss in Dechlorosoma suillum PS

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate Dsui_2799 Dsui_2799 oligopeptide/dipeptide ABC transporter, ATP-binding protein

Query= TCDB::Q97UG5
         (617 letters)



>FitnessBrowser__PS:Dsui_2799
          Length = 670

 Score =  396 bits (1017), Expect = e-114
 Identities = 238/619 (38%), Positives = 360/619 (58%), Gaps = 21/619 (3%)

Query: 5   MDSLLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKY 64
           M  LL V  L AG+      +  V  V+F V P E FA+ GESGCGKS  A+A+  LL  
Sbjct: 1   MSDLLSVRNLKAGFLAGGRVLTAVDGVSFAVAPGETFALLGESGCGKSATALALLRLLPN 60

Query: 65  PGVVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH 124
            G +  G V+L+ ++IL++ +  +R  R      + Q    +L+PV  IG Q+  +   H
Sbjct: 61  AGRIQGGEVWLEGEEILALPEAAMRDRRGSAAAMIFQEPATSLNPVLTIGRQIGESLERH 120

Query: 125 -GVNVEEARKLIKEKLELVDL--PYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDE 181
            G+  E AR+     L  V +  P   +  YP +LSGGM+QR +IA ++   P L+I DE
Sbjct: 121 RGMKGEAARREALALLTAVGIADPERRLEEYPFQLSGGMKQRAMIAIALAGEPRLLIADE 180

Query: 182 PTTGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKE 241
           PTT LDV +Q +IL  L R+Q +  + +++I+HD+ ++   + RVG+MYAGEIVE   ++
Sbjct: 181 PTTALDVTIQAQILDLLARLQAERAMGMLLITHDLGVVARSAHRVGVMYAGEIVETAPRQ 240

Query: 242 EIIKRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCS 301
           E    P HPYT  L ++LP L +R  +L +IPG  P  L+ +P  CRF  RCP  M++C 
Sbjct: 241 EFFASPRHPYTQKLFAALPDLGQRGAQLATIPGQVP-GLAAMPAGCRFAPRCPVAMDRCR 299

Query: 302 TLNPALGDIMDGHKARCF----LQKGGYVDLSTLPIPLEYYAEEKAETDLSESNQHEVVM 357
             +P   ++  GH+ RC        GG   L  LP      A   A  D +  N    ++
Sbjct: 300 LESPGWTELEAGHQVRCHWVAQQLPGGEQRLPDLPAAPPAAA---AAADAAREN----LL 352

Query: 358 KILNLSKIYYIRKNLILSE--PINAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMI 415
            +  L   + IRK L       + AV+ VS EL++G   ALVG SG GK+T  K +  ++
Sbjct: 353 AVGELKVHFPIRKGLFKRTVGHVKAVDGVSLELQRGRTLALVGESGCGKTTAGKAVLRLL 412

Query: 416 QQTSGKIILLGKDVSEYGVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKV 475
             T G + L G+++     R     +  +QM+FQDP++SL+PR TV   +E  +   +  
Sbjct: 413 PAT-GSVRLDGRELLGLPERELKPLRRRMQMVFQDPFASLNPRLTVGEIIEEGMTALRVA 471

Query: 476 SNKDQLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPV 535
           +++D+    +  +L++VGL  P + L +YPHE SGG+RQR+AIARA AV+P++LV DEP 
Sbjct: 472 ASRDERRAALAALLESVGL--PAEALGRYPHEFSGGQRQRIAIARALAVQPELLVCDEPT 529

Query: 536 SMLDASLRAGILNLIKKFKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEV 594
           S LD S++A ILNL+++ ++  G++ L+ITH+ A V Y+A ++ V+Y GRIVE+G   +V
Sbjct: 530 SALDVSVQAQILNLLRRLQEELGLAYLFITHNFAVVEYLAHDVAVMYLGRIVEQGPVQQV 589

Query: 595 ISNPSHEYTKRLIEAVPDP 613
           ++ P H YT+ L+ AVP+P
Sbjct: 590 LAAPCHPYTRALLSAVPEP 608



 Score =  178 bits (452), Expect = 6e-49
 Identities = 113/327 (34%), Positives = 177/327 (54%), Gaps = 21/327 (6%)

Query: 6   DSLLKVNELTA------GYFNQD-GFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAI 58
           ++LL V EL        G F +  G V  V  V+ E+      A+ GESGCGK+T   A+
Sbjct: 349 ENLLAVGELKVHFPIRKGLFKRTVGHVKAVDGVSLELQRGRTLALVGESGCGKTTAGKAV 408

Query: 59  YGLLKYPGVVLRGHVYLKDKDILSITQEELRKLRMK-EFVYVPQFAMDALDPVAKIGDQM 117
             LL        G V L  +++L + + EL+ LR + + V+   FA  +L+P   +G+ +
Sbjct: 409 LRLLP-----ATGSVRLDGRELLGLPERELKPLRRRMQMVFQDPFA--SLNPRLTVGEII 461

Query: 118 MRA--AVSHGVNVEEARKLIKEKLELVDLPYNVVNMYPHELSGGMRQRVVIATSILLNPS 175
                A+    + +E R  +   LE V LP   +  YPHE SGG RQR+ IA ++ + P 
Sbjct: 462 EEGMTALRVAASRDERRAALAALLESVGLPAEALGRYPHEFSGGQRQRIAIARALAVQPE 521

Query: 176 LIILDEPTTGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIV 235
           L++ DEPT+ LDV VQ +IL  L+R+Q +LG++ + I+H+ +++  ++  V +MY G IV
Sbjct: 522 LLVCDEPTSALDVSVQAQILNLLRRLQEELGLAYLFITHNFAVVEYLAHDVAVMYLGRIV 581

Query: 236 EIGSKEEIIKRPSHPYTYLLISSLPS--LVKRREKLLSIPGNPPLMLSKVPNSCRFYDRC 293
           E G  ++++  P HPYT  L+S++P   L  +RE ++ +PG  P   ++ P  C F+ RC
Sbjct: 582 EQGPVQQVLAAPCHPYTRALLSAVPEPRLAGQRE-MVRLPGETPSP-ARPPQGCHFHPRC 639

Query: 294 PFKMEKCSTLNPALGDIMDGHKARCFL 320
               E+C    PA      G   RC L
Sbjct: 640 AQASERCRQEYPAPSTQAGGVVVRCHL 666


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: 967
Number of extensions: 45
Number of successful extensions: 14
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: 670
Length adjustment: 38
Effective length of query: 579
Effective length of database: 632
Effective search space:   365928
Effective search space used:   365928
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.

Downloads

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

Related tools

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