Alignments for a candidate for malK_Ss in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for malK_Ss in Burkholderia phytofirmans PsJN

Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate BPHYT_RS15780 BPHYT_RS15780 ABC transporter ATP-binding protein

Query= TCDB::Q97UG5
         (617 letters)



>FitnessBrowser__BFirm:BPHYT_RS15780
          Length = 727

 Score =  332 bits (852), Expect = 3e-95
 Identities = 207/595 (34%), Positives = 340/595 (57%), Gaps = 31/595 (5%)

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

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

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

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

Query: 266 REKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLNP-------ALGDIMDGHKARC 318
            E+L +I G+ P     V   C + DRC    ++C    P       A GD M    +RC
Sbjct: 284 SERLDTIAGSLP-SPGSVTQGCIYADRCRLADDRCRREAPPPYRVSAARGDQM----SRC 338

Query: 319 FLQKGGYVDLSTLPIPLEYYAEEKAETDLSESNQHEVVMKILNLSKIYYIRKNLILSEPI 378
              +        LP        E+++  + +     +V++   LSK +++         +
Sbjct: 339 HYHERAI----DLPRASAEALPERSDAPV-DGKPPALVLRAERLSKTFHVS-----GAAL 388

Query: 379 NAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQTSGKIILL-GKDVSEYGVRNS 437
            AV++VS +L  G    LVG SG GK+T+AK++ G++   +G ++ L G  ++    R +
Sbjct: 389 RAVDNVSIDLASGETLGLVGESGSGKTTLAKLMLGLLTPDAGSVLELDGAPLAARVTRRN 448

Query: 438 MWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKNVGLKPP 497
               +++Q++FQ+P S+L+  H+V+  + R L   +  + +   + + +  L +  ++ P
Sbjct: 449 TEQVKSLQIVFQNPDSALNRAHSVKRLIGRAL--SRLTALRGPAIDERLAALTD-AVRLP 505

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

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



 Score =  155 bits (391), Expect = 7e-42
 Identities = 89/272 (32%), Positives = 156/272 (57%), Gaps = 14/272 (5%)

Query: 346 DLSESNQHEVVMKILNLSKIYYIRKNLILSEPINAVNDVSFELKKGTITALVGGSGHGKS 405
           D+S+S++ +  + ++ L+  Y IR           + D+SF +++G    LVG SG GKS
Sbjct: 13  DVSKSDRTDA-LTVVGLTVTYRIR-----GRDREVLQDISFRVRRGEAYGLVGESGCGKS 66

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

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

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

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



 Score =  145 bits (367), Expect = 5e-39
 Identities = 101/326 (30%), Positives = 165/326 (50%), Gaps = 21/326 (6%)

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

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

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

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

Query: 244 IKRPSHPYTYLLISSLPSL-VKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEK-CS 301
            + P HPYT  L+SS+P+L  +     + + G+ P   S  P+ C F+ RCP K+   C 
Sbjct: 604 FEGPHHPYTEALLSSVPTLDGQGGATRIHLSGDLPSAASP-PSGCVFHTRCPRKLGAICE 662

Query: 302 TLNPALGDIMDG-------HKARCFL 320
             +P   D  +G       H+ RC +
Sbjct: 663 QQDPPFVDAGEGEAAMPSAHRIRCHI 688


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: 963
Number of extensions: 54
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: 727
Length adjustment: 39
Effective length of query: 578
Effective length of database: 688
Effective search space:   397664
Effective search space used:   397664
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)
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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