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 (BgaB) (EC 3.2.1.23) (characterized)
to candidate BWI76_RS06715 BWI76_RS06715 beta-galactosidase

Query= CAZy::AEA30144.1
         (684 letters)



>FitnessBrowser__Koxy:BWI76_RS06715
          Length = 685

 Score = 1291 bits (3340), Expect = 0.0
 Identities = 607/685 (88%), Positives = 641/685 (93%), Gaps = 1/685 (0%)

Query: 1   MNKFAPLHPKVSTLLHGADYNPEQWENDPDIIDKDIAMMQQAKCNVMSVGIFSWAKLEPR 60
           M KFAPL PKV+ LLHGADYNPEQWEN PDIIDKDIAMMQQAKCNVMSVGIFSWAKLEP+
Sbjct: 1   MKKFAPLSPKVNALLHGADYNPEQWENYPDIIDKDIAMMQQAKCNVMSVGIFSWAKLEPQ 60

Query: 61  EGVFNFAWLDIILDKLYAAGIHVFLATPSGARPAWMSQRYPQVLRVGRDRVPALHGGRHN 120
           EGVF F WLD ILDKLYAAGIHVFLATPSGARPAWMSQ+YPQVLRVGRDRVPALHGGRHN
Sbjct: 61  EGVFEFGWLDSILDKLYAAGIHVFLATPSGARPAWMSQKYPQVLRVGRDRVPALHGGRHN 120

Query: 121 HCMSSPVYREKTLQINTLLAERYSSHPAVLGWHISNEYGGECHCDLCQNRFRDWLKARYQ 180
           HCMSSPVYREKTL+INTLLAERY+ HPAVLGWHISNEYGGECHC LCQ RFRDWLKARY+
Sbjct: 121 HCMSSPVYREKTLKINTLLAERYAQHPAVLGWHISNEYGGECHCSLCQERFRDWLKARYE 180

Query: 181 TLENLNQARWSTFWSHTYTDWSQIESPAPQGEMSIHGLNLDWHRFNTAQVTDFCRHEIAP 240
           TL+NLN A WSTFWSHTY+DWSQIESPAPQGE+SIHGLNLDWHRFNTAQVTDFCRHEIAP
Sbjct: 181 TLDNLNHAWWSTFWSHTYSDWSQIESPAPQGEVSIHGLNLDWHRFNTAQVTDFCRHEIAP 240

Query: 241 LKAANASLPVTTNFMEYFYDYDYWQLAEALDFISWDSYPMWHRDKDETALACYTAMYHDM 300
           LKAANA LPVTTNFMEYFYDYDYWQLA ALDFISWDSYPMWHRDKDET LACYTAMYHDM
Sbjct: 241 LKAANAELPVTTNFMEYFYDYDYWQLAPALDFISWDSYPMWHRDKDETTLACYTAMYHDM 300

Query: 301 MRSLKGGKPFVLMESTPGATNWQPTSKLKKPGMHILSSLQAVAHGADSVQYFQWRKSRGS 360
           MRSLKGGKPFVLMESTP ATNWQPTSKLKKPGMHILSSLQAVAHGADSVQYFQWRKSRGS
Sbjct: 301 MRSLKGGKPFVLMESTPSATNWQPTSKLKKPGMHILSSLQAVAHGADSVQYFQWRKSRGS 360

Query: 361 VEKFHGAVVDHVGHIDTRIGREVCQLGEILSKLPEVRGCRTEAKVAIIFDQQNRWALDNA 420
           VEKFHGA++DHVGH+DTR+GREV +LGE+LS+LP V GCRT+A+VAIIFDQQNRWALD+A
Sbjct: 361 VEKFHGAIIDHVGHLDTRVGREVTKLGEMLSQLPGVVGCRTDAQVAIIFDQQNRWALDDA 420

Query: 421 QGPRNLGMEYEKTVNEHYRPFWEQGIAVDVIDADVDLTPYQLVIAPMLYMVRDGFAGRAE 480
           QGPRNLGMEYE TVNEHYRPFWEQGIAVD+IDADVDL+ Y+LVIAPMLYMVRDGFA RAE
Sbjct: 421 QGPRNLGMEYENTVNEHYRPFWEQGIAVDIIDADVDLSAYRLVIAPMLYMVRDGFAERAE 480

Query: 481 AFVANGGHLVTTYWTGIVNESDLCYLGGFPGPLRNLLGIWAEEIDCLNDGEFNLVQGLAG 540
           AFVANGGHLVTTYWTGIVNESDLCYLGGFPGPLR LLGIWAEEIDCLNDGE NLVQGLAG
Sbjct: 481 AFVANGGHLVTTYWTGIVNESDLCYLGGFPGPLRKLLGIWAEEIDCLNDGERNLVQGLAG 540

Query: 541 NQCGLQGPYQVRHLCELIHIESAQALATYRDDFYAGRPAVTVNAFGKGKAWHVASRNDLA 600
           N+ GLQGPYQVRHLCELIH E+AQ LATYRDDFYAGRPAVTVN  GKGKAWHVASRNDLA
Sbjct: 541 NEGGLQGPYQVRHLCELIHAETAQPLATYRDDFYAGRPAVTVNHVGKGKAWHVASRNDLA 600

Query: 601 FQRDFFTALSKELALPRAIATELPPGVVATARTDGDNAFIFLQNYSAQNHTLTLPQGYRD 660
           FQRDFF+A+SKELALPRA+  + PPGVVATARTDG+  ++FLQNYSAQ   +TLPQGY+D
Sbjct: 601 FQRDFFSAISKELALPRAVEADFPPGVVATARTDGETTYVFLQNYSAQQQQVTLPQGYQD 660

Query: 661 CLTDAA-SAPLTLSAWDCRILRRHA 684
            LT  A +APL L AWDCRIL RHA
Sbjct: 661 TLTGTALNAPLILKAWDCRILSRHA 685


Lambda     K      H
   0.322    0.136    0.442 

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: 1795
Number of extensions: 54
Number of successful extensions: 2
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: 684
Length of database: 685
Length adjustment: 39
Effective length of query: 645
Effective length of database: 646
Effective search space:   416670
Effective search space used:   416670
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 (21.9 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)
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