Alignments for a candidate for H281DRAFT_01113 in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Klebsiella michiganensis M5al

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate BWI76_RS00660 BWI76_RS00660 ABC transporter

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>FitnessBrowser__Koxy:BWI76_RS00660
          Length = 503

 Score =  316 bits (809), Expect = 1e-90
 Identities = 177/498 (35%), Positives = 286/498 (57%), Gaps = 7/498 (1%)

Query: 12  SQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQ 71
           S P L + G+ K F GV AL  V L    G++  L+GENG GKSTL+K+++G   P+EG+
Sbjct: 4   STPLLSLKGITKVFPGVRALENVQLDLWPGKVTALIGENGAGKSTLVKVMTGIYQPEEGE 63

Query: 72  LVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRR 131
           ++ + +P    +   A   GI  ++Q+  L   +SV EN+ +   L  H G L +  D  
Sbjct: 64  ILYKAIPIQLPNPESAHKVGITAIHQETVLFDELSVTENIFVGQYL--HTG-LLKKLDWP 120

Query: 132 VLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLT 191
            +   A+  L  + +  +       ++ L +A R +VAIARA++ EA+ VI+DEPT +L+
Sbjct: 121 AMHRKASEILTRLEVQIDPR---ATLKTLSIAQRHMVAIARALSFEAQVVILDEPTAALS 177

Query: 192 QKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQI 251
           Q E+     ++  L+  G  +LF+SHK DE + +     +LRDG  ++ G I + T+ ++
Sbjct: 178 QHEILEFYQIVERLKQDGKAILFISHKFDEIFELADYYTILRDGVYVSSGAINDITEERM 237

Query: 252 SELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRN 311
             +M GR ++    +      + VL+V+      +F+ +SF L  GEILG  GL+ +GR 
Sbjct: 238 VAMMVGRAITQTYPKVDCIPGETVLEVKDLCHPTEFAHISFSLRKGEILGFYGLVGAGRT 297

Query: 312 ELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVI 371
           EL +AL+GV+   SGD++L G+ +  R P+DA    I  VPE+R  +G  +  PI  N+ 
Sbjct: 298 ELMQALSGVSHPSSGDIVLKGKPMRFRQPADAISAGIVCVPEERQKQGAIIALPIAQNIS 357

Query: 372 TAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAI 431
              +S L    G ++  R   LA++    LQ+      + V++LSGGNQQ+V+IG+WLA 
Sbjct: 358 LPQLSKLNPG-GVLNDAREWRLADEYASRLQVKAFSWRQAVETLSGGNQQKVVIGKWLAT 416

Query: 432 DPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGH 491
            P V+IL  PT G+D+GSK  +++ M  L  +G+ +I++S +LPE++   DRI++M +G 
Sbjct: 417 HPEVIILDEPTKGIDIGSKAAVHQFMSELVSQGLAVIMVSSELPEVMGMADRIIVMHEGL 476

Query: 492 VSAEYRADELSEADLYHA 509
           + AEYRA E +   +  A
Sbjct: 477 MVAEYRAGEATAETIVSA 494



 Score = 76.3 bits (186), Expect = 3e-18
 Identities = 56/227 (24%), Positives = 103/227 (45%), Gaps = 8/227 (3%)

Query: 34  VSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAAGIE 93
           +S S ++G+I    G  G G++ L++ +SG   P  G +V++G P       +A++AGI 
Sbjct: 276 ISFSLRKGEILGFYGLVGAGRTELMQALSGVSHPSSGDIVLKGKPMRFRQPADAISAGIV 335

Query: 94  TV---YQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALEAVGLPGNS 150
            V    Q    +  + +A+N++L      + G +        LA   A  L+        
Sbjct: 336 CVPEERQKQGAIIALPIAQNISLPQLSKLNPGGVLNDAREWRLADEYASRLQVKAFSWRQ 395

Query: 151 EFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQGV 210
                 +E L    +Q V I + +A+  + +I+DEPT  +       +   ++ L +QG+
Sbjct: 396 A-----VETLSGGNQQKVVIGKWLATHPEVIILDEPTKGIDIGSKAAVHQFMSELVSQGL 450

Query: 211 TVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTG 257
            V+ VS +L E   +   +IV+ +G  +A+    E T   I    +G
Sbjct: 451 AVIMVSSELPEVMGMADRIIVMHEGLMVAEYRAGEATAETIVSAASG 497



 Score = 56.2 bits (134), Expect = 3e-12
 Identities = 48/244 (19%), Positives = 106/244 (43%), Gaps = 9/244 (3%)

Query: 275 VLDVRGFTRA----GQFSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLL 330
           +L ++G T+         +V   L  G++  + G   +G++ L + + G+   + G++L 
Sbjct: 7   LLSLKGITKVFPGVRALENVQLDLWPGKVTALIGENGAGKSTLVKVMTGIYQPEEGEILY 66

Query: 331 DGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRA 390
               I L  P  A +  I  + ++ +   LF +  + +N+             ++D    
Sbjct: 67  KAIPIQLPNPESAHKVGITAIHQETV---LFDELSVTENIFVGQYLHT-GLLKKLDWPAM 122

Query: 391 QALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSK 450
              A + +  L++        +++LS   +  V I R L+ + +V+IL  PT  +     
Sbjct: 123 HRKASEILTRLEVQIDP-RATLKTLSIAQRHMVAIARALSFEAQVVILDEPTAALSQHEI 181

Query: 451 DIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHAL 510
              Y+I++RL Q G  I+ IS    E+ +  D   +++ G   +    ++++E  +   +
Sbjct: 182 LEFYQIVERLKQDGKAILFISHKFDEIFELADYYTILRDGVYVSSGAINDITEERMVAMM 241

Query: 511 LSEA 514
           +  A
Sbjct: 242 VGRA 245


Lambda     K      H
   0.319    0.135    0.376 

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: 562
Number of extensions: 22
Number of successful extensions: 7
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: 515
Length of database: 503
Length adjustment: 34
Effective length of query: 481
Effective length of database: 469
Effective search space:   225589
Effective search space used:   225589
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: 52 (24.6 bits)

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

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Protein sequences (fasta format)
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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