Alignments for a candidate for BPHYT_RS34245 in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS34245 in Klebsiella michiganensis M5al

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__Koxy:BWI76_RS14860
          Length = 510

 Score =  296 bits (759), Expect = 9e-85
 Identities = 181/501 (36%), Positives = 281/501 (56%), Gaps = 13/501 (2%)

Query: 10  SSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTG 69
           SS P++    ++KR+G+T ALN+V   +  GE HAL+G NGAGKSTL+ IL+G  + D+G
Sbjct: 5   SSPPLLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSG 64

Query: 70  EVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLR-GGVIDWQAMR 128
            +   G A      RDA +  +A ++Q    + D++VAENLF+ ++P    G++D + M 
Sbjct: 65  VIFIDGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRMH 124

Query: 129 RDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKR 188
           R+A+  L+    D+   A  G LS+  +Q+VEIARA+S  A+ ++LDEPTA L   E  +
Sbjct: 125 REAKEKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQ 184

Query: 189 LFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG 248
           L+R I++++++GV  ++ISH ++EV+++   VTV RD   I +  +  +    ++  M G
Sbjct: 185 LYRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMVG 244

Query: 249 ERGGLAVADAAARGALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSV 308
            +    V         P D  V LE+++L G+    VSF V  GEVV ++G   SGRT V
Sbjct: 245 RQ---IVDLYQHEPRTPGD--VLLEVRDLAGSATGPVSFEVSAGEVVSMSGLVGSGRTEV 299

Query: 309 AEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMT 368
           A  + G     +G++ + G    P D  A++A GIG V +DR  +GL L  SV  N  ++
Sbjct: 300 ARLLFGADPRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDIS 359

Query: 369 IARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPN 428
                   G+       A   + +  L +     E  VS LSGGNQQK  +AR L  +  
Sbjct: 360 SLDNFVAGGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSR 419

Query: 429 VLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAA 487
           +L+L +PT GVD+ +K  +  ++DR+   GKA+LV+S +L + +   DRVLVM  GR+  
Sbjct: 420 LLILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVH 479

Query: 488 EFPAGWQDHDLIASVEGVSLH 508
           + P+        A+ E V LH
Sbjct: 480 QLPS------CSATEEEVMLH 494



 Score = 65.5 bits (158), Expect = 4e-15
 Identities = 67/239 (28%), Positives = 104/239 (43%), Gaps = 12/239 (5%)

Query: 18  LEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAA 77
           LEV    GS  A   VS  V  GE  ++ G  G+G++ +  +L G      G VR +G  
Sbjct: 263 LEVRDLAGS--ATGPVSFEVSAGEVVSMSGLVGSGRTEVARLLFGADPRSQGSVRLAGRE 320

Query: 78  APSIADRDAWRERVACVYQHST---IIRDLSVAENLFINRQP--LRGGVIDWQAMRRDAR 132
           +       A  + +  V +      +    SV  N+ I+     + GGV+  + +R  A 
Sbjct: 321 SQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSLDNFVAGGVVKRKTIR--AA 378

Query: 133 ALLDHWKIDVREDA---RAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRL 189
            L    ++ +RE+A       LS   +Q   +AR L   +R +ILDEPT  +D    + +
Sbjct: 379 VLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLLILDEPTRGVDIGAKREI 438

Query: 190 FRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG 248
           +  I  L R G   L IS  L E   I   V V+R  R +   P  +   E+++   TG
Sbjct: 439 YELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQLPSCSATEEEVMLHATG 497


Lambda     K      H
   0.318    0.134    0.377 

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: 632
Number of extensions: 22
Number of successful extensions: 8
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: 510
Length of database: 510
Length adjustment: 34
Effective length of query: 476
Effective length of database: 476
Effective search space:   226576
Effective search space used:   226576
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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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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