Alignments for a candidate for lacZ in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Klebsiella michiganensis M5al

Align β-galactosidase (LacZ) (EC 3.2.1.23) (characterized)
to candidate BWI76_RS15420 BWI76_RS15420 beta-D-galactosidase

Query= CAZy::AEA30145.1
         (1035 letters)



>FitnessBrowser__Koxy:BWI76_RS15420
          Length = 1035

 Score = 1760 bits (4558), Expect = 0.0
 Identities = 816/1032 (79%), Positives = 895/1032 (86%)

Query: 1    MQISDTGRSHTPDFHAVLAREDWQNQSITHLNRLPAHPVFASWRDELAARDNLPSSRRRQ 60
            MQ  D+  +    FH VL REDWQNQ+ITHLNRLPAHP FASWRD  AAR+N PS+ RR+
Sbjct: 1    MQQHDSISAAGATFHQVLVREDWQNQTITHLNRLPAHPTFASWRDPDAARENRPSASRRR 60

Query: 61   LDGEWQFSYARSPFAVDAQWLTQDLPDCRGTPVPSNWQMEGYDAPIYTNVRYPIDTTPPR 120
            LDG+WQFS ARSPFAVDA+WL  DLPD R TPVPSNWQMEGYDAPIYTNVRYPIDTTPPR
Sbjct: 61   LDGQWQFSLARSPFAVDARWLEDDLPDSRSTPVPSNWQMEGYDAPIYTNVRYPIDTTPPR 120

Query: 121  VPEDNPTGCYSLHFTVEDTWRENGQTQIIFDGVNSAFHLWCNGVWVGYSQDSRLPAAFDL 180
            VPE+NPTGCYSL F+V++ W+ NGQTQIIFDGVNSAFHLWCNG WVGYSQDSRLPAAFDL
Sbjct: 121  VPEENPTGCYSLTFSVDEDWQANGQTQIIFDGVNSAFHLWCNGEWVGYSQDSRLPAAFDL 180

Query: 181  SPFLRPGDNRLCVMVMRWSAGSWLEDQDMWRMSGIFRSVWLLNKPQQRLCDVQLTPALDA 240
            SPFL+PGDNR+CVMVMRWSAG+WLEDQDMWRMSGIFRSVWLLNKP   L DVQLTP LDA
Sbjct: 181  SPFLQPGDNRICVMVMRWSAGTWLEDQDMWRMSGIFRSVWLLNKPTLHLSDVQLTPQLDA 240

Query: 241  LYRDGTLQVQATIEATEAALAGLSVGVSLWRGEEQIAAGRQPLGTPTVDERGHYAERVDF 300
            LYRD  L V  ++ A  A L  L+V V LW  +  +A+ RQP G+P +DERG+YAER   
Sbjct: 241  LYRDAELLVNVSVAAPVAQLEELTVKVELWDEDRLVASHRQPPGSPIIDERGNYAERAAI 300

Query: 301  SLAVATPAHWSAETPNCYRAVVTLWRGDELLEAEAWDIGFRRIEIADGLLRLNGKPLLIR 360
             L V  PA WSAETPNCYRAVV+LWRGDE +EAEAWDIGFRR+EI +GLL LNGKPLLIR
Sbjct: 301  RLPVEKPALWSAETPNCYRAVVSLWRGDETIEAEAWDIGFRRVEIKNGLLLLNGKPLLIR 360

Query: 361  GVNRHEHHHLRGQVVTEADMVQDILLMKQNNFNAVRCSHYPNAPRWYELCNRYGLYVVDE 420
            GVNRHEHHH RGQVVTE DMVQDILLMKQNNFNAVRCSHYPNAPRWYELCNRYGLYVVDE
Sbjct: 361  GVNRHEHHHQRGQVVTEEDMVQDILLMKQNNFNAVRCSHYPNAPRWYELCNRYGLYVVDE 420

Query: 421  ANIETHGMVPMNRLSDDPAWLPAFSARVTRMVQSNRNHPCIIIWSLGNESGGGGNHEALY 480
            ANIETHGMVPMNRLSDDPAWLPAFSARV+RM+QSNRNHP IIIWSLGNESGGGGNHEA+Y
Sbjct: 421  ANIETHGMVPMNRLSDDPAWLPAFSARVSRMLQSNRNHPSIIIWSLGNESGGGGNHEAMY 480

Query: 481  HWLKRNDPSRPVQYEGGGADTTATDIICPMYARVERDQPIPAVPKWGIKKWISLPGEQRP 540
            HWLKRNDPSRPVQYEGGGAD+T TDIICPMYARVERDQ IP VPKWGIKKWISLPGEQRP
Sbjct: 481  HWLKRNDPSRPVQYEGGGADSTTTDIICPMYARVERDQLIPTVPKWGIKKWISLPGEQRP 540

Query: 541  LILCEYAHAMGNSLGNFADYWQAFREYPRLQGGFIWDWADQAIRKTFADGSVGWAYGGDF 600
            LILCEYAHAMGNSLGNFADYWQAFR+YPRLQGGFIWDWADQAI KTF DGSVG+AYGGDF
Sbjct: 541  LILCEYAHAMGNSLGNFADYWQAFRDYPRLQGGFIWDWADQAISKTFDDGSVGYAYGGDF 600

Query: 601  GDKPNDRQFCMNGLVFPDRTPHPSLVEAKHAQQYFQFTLLSTSPLRVRIISEYLFRPTDN 660
            GDKPNDRQFCMNGLVFPDR PHPSL+EAKHAQQYFQF LL+ SPLR+ + SEYLFR TDN
Sbjct: 601  GDKPNDRQFCMNGLVFPDRRPHPSLIEAKHAQQYFQFALLAQSPLRIGVSSEYLFRATDN 660

Query: 661  EVLRWQVQAAGEPLYHGDLTLALPPEGSDEITLLDSLILPEGARAVWLTLEVTQPQATAW 720
            E LRWQVQAAGE    G + L L PEG  E+TL ++L LP GA  +WLTLEV QPQATAW
Sbjct: 661  EELRWQVQAAGETFAEGQVKLELSPEGQSELTLCEALALPAGAEEIWLTLEVVQPQATAW 720

Query: 721  SEAEHRVAWQQFPLPAPLALQAPTVSAGAPDLIVSDEVWQIRAGSQCWTIDRRTGLLSRW 780
            S+A HRVAWQQFP+ APLAL+ P  +  AP L  SD  W +R+G+Q WT+DR +GLL+RW
Sbjct: 721  SDAGHRVAWQQFPIAAPLALRRPAPTGTAPALDGSDAAWTVRSGAQQWTVDRESGLLTRW 780

Query: 781  SVGGQEQLLTPLRDQFIRAPLDNDIGVSEVERIDPNAWVERWKSAGLYDLEAHCVQCDAQ 840
             V G EQLLTPLRDQF+RAPLDNDIGVSEVERIDPNAWVERWKSAGLY L A CV CDAQ
Sbjct: 781  QVDGVEQLLTPLRDQFVRAPLDNDIGVSEVERIDPNAWVERWKSAGLYGLSARCVACDAQ 840

Query: 841  RLANETLVDCRWHYLRGEEVVIVSHWRMHFTADGTLRLAVDGERAETLPPLPRVGLHFQV 900
            RLA+E ++D RWHYLRG+EVVIVSHWRM F ++G L LAVDGERA TLPPLPR+GL FQV
Sbjct: 841  RLAHEVVIDSRWHYLRGDEVVIVSHWRMTFDSEGKLHLAVDGERAGTLPPLPRIGLTFQV 900

Query: 901  ADQQAPVSWLGLGPHENYPDRRSSACFARWEQPLAAMTTPYIFPTENGLRCDTQALDWGR 960
             DQQ PVSWLG GPHENYPDRR+SACF+RW+ PL  MTTPYIFPTENGLRCD++ALDWGR
Sbjct: 901  PDQQQPVSWLGYGPHENYPDRRTSACFSRWQLPLEEMTTPYIFPTENGLRCDSKALDWGR 960

Query: 961  WHISGHFHFSVQPWSTSQLMETDHWHKMQAEDGVWITLDGLHMGVGGDDSWTPSVLPQWL 1020
            WH+ G FHFSVQP+ST+QLMETDHWH+M+ E GVWI LD  HMG+GGDDSWTPSVL QWL
Sbjct: 961  WHVGGDFHFSVQPYSTAQLMETDHWHRMKPEKGVWIALDAQHMGIGGDDSWTPSVLQQWL 1020

Query: 1021 LSQTRWQYEVSL 1032
            L + +WQY++++
Sbjct: 1021 LLERQWQYQLTI 1032


Lambda     K      H
   0.321    0.136    0.455 

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: 4715
Number of extensions: 251
Number of successful extensions: 4
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: 1035
Length of database: 1035
Length adjustment: 45
Effective length of query: 990
Effective length of database: 990
Effective search space:   980100
Effective search space used:   980100
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: 57 (26.6 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

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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