Alignments for a candidate for lacL in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacL in Klebsiella michiganensis M5al

Align LVIS_2259 + LVIS_2258 (EC 3.2.1.23) (characterized)
to candidate BWI76_RS15420 BWI76_RS15420 beta-D-galactosidase

Query= CAZy::ABJ65308.1
         (628 letters)



>FitnessBrowser__Koxy:BWI76_RS15420
          Length = 1035

 Score =  338 bits (868), Expect = 5e-97
 Identities = 218/629 (34%), Positives = 315/629 (50%), Gaps = 51/629 (8%)

Query: 16  INQLPAHSDHRGYASVEEATAQHSSLVQS-LDGTWQFAFAPDPVHRFEGFYQPDYDRSAF 74
           +N+LPAH     +   + A     S  +  LDG WQF+ A  P      + + D   S  
Sbjct: 31  LNRLPAHPTFASWRDPDAARENRPSASRRRLDGQWQFSLARSPFAVDARWLEDDLPDSR- 89

Query: 75  DRLTVPGHIELAGYGQIQYINTAYPWEGHHYRRPAYSMGADQPEKGMFSTDPQNTVGAYV 134
               VP + ++ GY    Y N  YP +    R P                  +N  G Y 
Sbjct: 90  -STPVPSNWQMEGYDAPIYTNVRYPIDTTPPRVPE-----------------ENPTGCYS 131

Query: 135 KHFTLNPAL-ANQRVSIEFDGVEQAMFLWLNGQFVGYAEDSFSRSEFDLTPYLQAGQNLL 193
             F+++    AN +  I FDGV  A  LW NG++VGY++DS   + FDL+P+LQ G N +
Sbjct: 132 LTFSVDEDWQANGQTQIIFDGVNSAFHLWCNGEWVGYSQDSRLPAAFDLSPFLQPGDNRI 191

Query: 194 AVEVFKHSTAAFLEDQDMFRFSGIFRSVRLVAKPELHVEDLTIRAGLDDAFQTGDLKVRL 253
            V V + S   +LEDQDM+R SGIFRSV L+ KP LH+ D+ +   LD  ++  +L V +
Sbjct: 192 CVMVMRWSAGTWLEDQDMWRMSGIFRSVWLLNKPTLHLSDVQLTPQLDALYRDAELLVNV 251

Query: 254 QLTA-ASQLSGTATAQLLTADGQEVWATEQPAASTL-----------DLAAAIDHVHLWD 301
            + A  +QL        L  + + V +  QP  S +            +   ++   LW 
Sbjct: 252 SVAAPVAQLEELTVKVELWDEDRLVASHRQPPGSPIIDERGNYAERAAIRLPVEKPALWS 311

Query: 302 HHDPYLYQLRITLKDVAGQVVEVVPYPVGFRRIELKDKVMCLNGQRLILNGVNRHEWDAH 361
              P  Y+  ++L     + +E   + +GFRR+E+K+ ++ LNG+ L++ GVNRHE    
Sbjct: 312 AETPNCYRAVVSLWR-GDETIEAEAWDIGFRRVEIKNGLLLLNGKPLLIRGVNRHEHHHQ 370

Query: 362 RGRAVTMADMTQDLQTFHDNHINAVRTCHYPDQDAWYYLCDQQGIYMMAENNLETHGTWQ 421
           RG+ VT  DM QD+     N+ NAVR  HYP+   WY LC++ G+Y++ E N+ETHG   
Sbjct: 371 RGQVVTEEDMVQDILLMKQNNFNAVRCSHYPNAPRWYELCNRYGLYVVDEANIETHG--- 427

Query: 422 KMGAVEPSYNVPGSLPQWQLAVLDRAKSNYEMFKNHPAVLFWSLGNESYAGDNIAAMDAF 481
            M  +    + P  LP +   V    +SN    +NHP+++ WSLGNES  G N  AM  +
Sbjct: 428 -MVPMNRLSDDPAWLPAFSARVSRMLQSN----RNHPSIIIWSLGNESGGGGNHEAMYHW 482

Query: 482 YHHADPTRLTHYEGVCRNRVYEDRISDMESMMYD-------PPRAIEDYLK-NDPQKPFV 533
               DP+R   YEG   +    D I  M + +         P   I+ ++     Q+P +
Sbjct: 483 LKRNDPSRPVQYEGGGADSTTTDIICPMYARVERDQLIPTVPKWGIKKWISLPGEQRPLI 542

Query: 534 NCEYMHDMGNSLGGMASYDALIDQYPMYQGGFIWDFIDQALWVKDEVTGQPVLRYGGDFD 593
            CEY H MGNSLG  A Y      YP  QGGFIWD+ DQA+  K    G     YGGDF 
Sbjct: 543 LCEYAHAMGNSLGNFADYWQAFRDYPRLQGGFIWDWADQAI-SKTFDDGSVGYAYGGDFG 601

Query: 594 DRHSDYEFSGDGLLFADRTPKPALQEVDY 622
           D+ +D +F  +GL+F DR P P+L E  +
Sbjct: 602 DKPNDRQFCMNGLVFPDRRPHPSLIEAKH 630


Lambda     K      H
   0.320    0.136    0.428 

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: 1992
Number of extensions: 109
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 628
Length of database: 1035
Length adjustment: 41
Effective length of query: 587
Effective length of database: 994
Effective search space:   583478
Effective search space used:   583478
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 (21.8 bits)
S2: 56 (26.2 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