Alignments for a candidate for malK_Ss in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for malK_Ss in Paraburkholderia bryophila 376MFSha3.1

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate H281DRAFT_04094 H281DRAFT_04094 peptide/nickel transport system ATP-binding protein

Query= TCDB::Q97UG5
         (617 letters)



>FitnessBrowser__Burk376:H281DRAFT_04094
          Length = 744

 Score =  337 bits (865), Expect = 8e-97
 Identities = 213/595 (35%), Positives = 340/595 (57%), Gaps = 31/595 (5%)

Query: 30  NVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVVLRGHVYLKDKDILSITQEELR 89
           +V+F V   E + + GESGCGKST+AMA    L   G V  G + +   D+  +  + LR
Sbjct: 44  DVSFRVRRGEAYGLVGESGCGKSTVAMAALRYLPRNGKVKAGKIVIAGADVNKLDADALR 103

Query: 90  KLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSHGVNVEEARKLIKEKLELVDL--PYN 147
            +R      V Q    AL+P   I  Q+  A  + GV  +EA +   E L+ V +  P  
Sbjct: 104 TMRANTISMVYQDPARALNPSLTIARQVSEAFEAAGVAPDEALQRSLEMLQRVRIASPER 163

Query: 148 VVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTTGLDVIVQYEILKDLKRIQRQLGV 207
           V++ YPH+LSGGM+QRVVIA ++  NP+L+ILDEPTTGLD  V+ E+L  + +++ +LG 
Sbjct: 164 VMDSYPHQLSGGMQQRVVIAMALASNPALLILDEPTTGLDATVEAEVLDLVAQLRAELGT 223

Query: 208 SLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIKRPSHPYTYLLISSLPSL--VKR 265
           +++ ISH+++++  + +RVG++YAG++VE G+ +++  RP HPYT  L+  LP++   K 
Sbjct: 224 AVLFISHNLAVIGRMCERVGVLYAGKLVEEGATQDVFTRPRHPYTVGLLRCLPTVGRSKD 283

Query: 266 REKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLNPALGDIMDGH---KARCFLQK 322
            E+L +I G  P     V   C + +RC    ++C    P    +   H    +RC   +
Sbjct: 284 TERLDTIAGGLP-SPGSVTQGCIYAERCRLADDRCRREAPPPYRVSAAHGDQMSRCHYHE 342

Query: 323 GGYVDLSTLPIPLEYYAEEKAETDL--SESNQHEVVMKILNLSKIYYIRKNLILSEPINA 380
                   LP  L   A+   E DL  ++ N  E+V++  NLSK +++         + A
Sbjct: 343 RAI----ELPRAL---AQALPEHDLANADKNPRELVLRAENLSKTFHVS-----GTALRA 390

Query: 381 VNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQTSGKIILL-GKDVSEYGVRNSMW 439
           V+ VS +L  G    LVG SG GK+T+AK++ G++   +G ++ L G  ++    R +  
Sbjct: 391 VDKVSLDLAAGETLGLVGESGSGKTTLAKLMLGLLAPDAGSVLELDGAPLAARVTRRNDE 450

Query: 440 YKENVQMIFQDPYSSLDPRHTVRWHVERPL--LIHKKVSNKDQLLPKIIEVLKNVGLKPP 497
             +++Q++FQ+P S+L+  H+V+  + R L  L   + +  D+ L  +        ++ P
Sbjct: 451 QVKSLQIVFQNPDSALNRAHSVKRLIGRALSRLAALRGAAIDERLATL-----TAAVRLP 505

Query: 498 EKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKKF-KKN 556
           E+YL     +LSGG +QRVAIARA A EP+V+V DEP S LD S++A ILNL+    ++ 
Sbjct: 506 ERYLGSRTRQLSGGLKQRVAIARAFAGEPRVVVCDEPTSALDVSVQAAILNLLADLQRER 565

Query: 557 GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611
           G+S ++I+HD+  V Y++D I V+Y GR++E G    V   P H YT+ L+ +VP
Sbjct: 566 GVSYVFISHDLHVVRYLSDRIAVLYLGRLLEIGPAAAVFDGPQHPYTEALLSSVP 620



 Score =  150 bits (379), Expect = 2e-40
 Identities = 87/272 (31%), Positives = 154/272 (56%), Gaps = 14/272 (5%)

Query: 346 DLSESNQHEVVMKILNLSKIYYIRKNLILSEPINAVNDVSFELKKGTITALVGGSGHGKS 405
           D+S+S++ +  + ++ L+  Y +R           + DVSF +++G    LVG SG GKS
Sbjct: 13  DVSKSDRTDA-LTVVGLTVTYRMR-----GRDREVLQDVSFRVRRGEAYGLVGESGCGKS 66

Query: 406 TIAKILAGMIQQT----SGKIILLGKDVSEYGVRNSMWYKEN-VQMIFQDPYSSLDPRHT 460
           T+A      + +     +GKI++ G DV++         + N + M++QDP  +L+P  T
Sbjct: 67  TVAMAALRYLPRNGKVKAGKIVIAGADVNKLDADALRTMRANTISMVYQDPARALNPSLT 126

Query: 461 VRWHVERPLLIHKKVSNKDQLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIAR 520
           +   V             D+ L + +E+L+ V +  PE+ +  YPH+LSGG +QRV IA 
Sbjct: 127 IARQVSE--AFEAAGVAPDEALQRSLEMLQRVRIASPERVMDSYPHQLSGGMQQRVVIAM 184

Query: 521 ATAVEPKVLVADEPVSMLDASLRAGILNLIKKFKKN-GISILYITHDIATVNYIADEIMV 579
           A A  P +L+ DEP + LDA++ A +L+L+ + +   G ++L+I+H++A +  + + + V
Sbjct: 185 ALASNPALLILDEPTTGLDATVEAEVLDLVAQLRAELGTAVLFISHNLAVIGRMCERVGV 244

Query: 580 IYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611
           +Y G++VE+G T +V + P H YT  L+  +P
Sbjct: 245 LYAGKLVEEGATQDVFTRPRHPYTVGLLRCLP 276



 Score =  140 bits (353), Expect = 2e-37
 Identities = 98/311 (31%), Positives = 156/311 (50%), Gaps = 14/311 (4%)

Query: 8   LLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGV 67
           +L+   L+  +      +  V  V+ ++   E   + GESG GK+TLA  + GLL     
Sbjct: 371 VLRAENLSKTFHVSGTALRAVDKVSLDLAAGETLGLVGESGSGKTTLAKLMLGLLAPDA- 429

Query: 68  VLRGHVYLKDKDILS--ITQEELRKLRMKEFVYV-PQFAMDALDPVAK-IGDQMMRAAVS 123
              G V   D   L+  +T+    +++  + V+  P  A++    V + IG  + R A  
Sbjct: 430 ---GSVLELDGAPLAARVTRRNDEQVKSLQIVFQNPDSALNRAHSVKRLIGRALSRLAAL 486

Query: 124 HGVNVEEARKLIKEKLELVDLPYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPT 183
            G  ++E    +      V LP   +     +LSGG++QRV IA +    P +++ DEPT
Sbjct: 487 RGAAIDERLATLTAA---VRLPERYLGSRTRQLSGGLKQRVAIARAFAGEPRVVVCDEPT 543

Query: 184 TGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEI 243
           + LDV VQ  IL  L  +QR+ GVS V ISHD+ ++  +SDR+ ++Y G ++EIG    +
Sbjct: 544 SALDVSVQAAILNLLADLQRERGVSYVFISHDLHVVRYLSDRIAVLYLGRLLEIGPAAAV 603

Query: 244 IKRPSHPYTYLLISSLPSLVKRRE-KLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEK-CS 301
              P HPYT  L+SS+P+L        + + G+ P   S  P+ C F+ RCP K+   C 
Sbjct: 604 FDGPQHPYTEALLSSVPTLDGHASVARVRLSGDLPSAASP-PSGCVFHTRCPRKLGAICE 662

Query: 302 TLNPALGDIMD 312
             +P   +  D
Sbjct: 663 QQDPPFAEAAD 673


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: 981
Number of extensions: 52
Number of successful extensions: 13
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 617
Length of database: 744
Length adjustment: 39
Effective length of query: 578
Effective length of database: 705
Effective search space:   407490
Effective search space used:   407490
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