Alignments for a candidate for lacZ in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Escherichia coli BW25113

Align Evolved beta-galactosidase subunit alpha; Beta-gal; Lactase; EC 3.2.1.23 (characterized)
to candidate 1936924 b3076 cryptic beta-D-galactosidase, alpha subunit (NCBI)

Query= SwissProt::P06864
         (1030 letters)



>FitnessBrowser__Keio:1936924
          Length = 1030

 Score = 2161 bits (5600), Expect = 0.0
 Identities = 1030/1030 (100%), Positives = 1030/1030 (100%)

Query: 1    MNRWENIQLTHENRLAPRAYFFSYDSVAQARTFARETSSLFLPLSGQWNFHFFDHPLQVP 60
            MNRWENIQLTHENRLAPRAYFFSYDSVAQARTFARETSSLFLPLSGQWNFHFFDHPLQVP
Sbjct: 1    MNRWENIQLTHENRLAPRAYFFSYDSVAQARTFARETSSLFLPLSGQWNFHFFDHPLQVP 60

Query: 61   EAFTSELMADWGHITVPAMWQMEGHGKLQYTDEGFPFPIDVPFVPSDNPTGAYQRIFTLS 120
            EAFTSELMADWGHITVPAMWQMEGHGKLQYTDEGFPFPIDVPFVPSDNPTGAYQRIFTLS
Sbjct: 61   EAFTSELMADWGHITVPAMWQMEGHGKLQYTDEGFPFPIDVPFVPSDNPTGAYQRIFTLS 120

Query: 121  DGWQGKQTLIKFDGVETYFEVYVNGQYVGFSKGSRLTAEFDISAMVKTGDNLLCVRVMQW 180
            DGWQGKQTLIKFDGVETYFEVYVNGQYVGFSKGSRLTAEFDISAMVKTGDNLLCVRVMQW
Sbjct: 121  DGWQGKQTLIKFDGVETYFEVYVNGQYVGFSKGSRLTAEFDISAMVKTGDNLLCVRVMQW 180

Query: 181  ADSTYVEDQDMWWSAGIFRDVYLVGKHLTHINDFTVRTDFDEAYCDATLSCEVVLENLAA 240
            ADSTYVEDQDMWWSAGIFRDVYLVGKHLTHINDFTVRTDFDEAYCDATLSCEVVLENLAA
Sbjct: 181  ADSTYVEDQDMWWSAGIFRDVYLVGKHLTHINDFTVRTDFDEAYCDATLSCEVVLENLAA 240

Query: 241  SPVVTTLEYTLFDGERVVHSSAIDHLAIEKLTSASFAFTVEQPQQWSAESPYLYHLVMTL 300
            SPVVTTLEYTLFDGERVVHSSAIDHLAIEKLTSASFAFTVEQPQQWSAESPYLYHLVMTL
Sbjct: 241  SPVVTTLEYTLFDGERVVHSSAIDHLAIEKLTSASFAFTVEQPQQWSAESPYLYHLVMTL 300

Query: 301  KDANGNVLEVVPQRVGFRDIKVRDGLFWINNRYVMLHGVNRHDNDHRKGRAVGMDRVEKD 360
            KDANGNVLEVVPQRVGFRDIKVRDGLFWINNRYVMLHGVNRHDNDHRKGRAVGMDRVEKD
Sbjct: 301  KDANGNVLEVVPQRVGFRDIKVRDGLFWINNRYVMLHGVNRHDNDHRKGRAVGMDRVEKD 360

Query: 361  LQLMKQHNINSVRTAHYPNDPRFYELCDIYGLFVMAETDVESHGFANVGDISRITDDPQW 420
            LQLMKQHNINSVRTAHYPNDPRFYELCDIYGLFVMAETDVESHGFANVGDISRITDDPQW
Sbjct: 361  LQLMKQHNINSVRTAHYPNDPRFYELCDIYGLFVMAETDVESHGFANVGDISRITDDPQW 420

Query: 421  EKVYVERIVRHIHAQKNHPSIIIWSLGNESGYGCNIRAMYHAAKALDDTRLVHYEEDRDA 480
            EKVYVERIVRHIHAQKNHPSIIIWSLGNESGYGCNIRAMYHAAKALDDTRLVHYEEDRDA
Sbjct: 421  EKVYVERIVRHIHAQKNHPSIIIWSLGNESGYGCNIRAMYHAAKALDDTRLVHYEEDRDA 480

Query: 481  EVVDIISTMYTRVPLMNEFGEYPHPKPRIICEYAHAMGNGPGGLTEYQNVFYKHDCIQGH 540
            EVVDIISTMYTRVPLMNEFGEYPHPKPRIICEYAHAMGNGPGGLTEYQNVFYKHDCIQGH
Sbjct: 481  EVVDIISTMYTRVPLMNEFGEYPHPKPRIICEYAHAMGNGPGGLTEYQNVFYKHDCIQGH 540

Query: 541  YVWEWCDHGIQAQDDHGNVWYKFGGDYGDYPNNYNFCLDGLIYSDQTPGPGLKEYKQVIA 600
            YVWEWCDHGIQAQDDHGNVWYKFGGDYGDYPNNYNFCLDGLIYSDQTPGPGLKEYKQVIA
Sbjct: 541  YVWEWCDHGIQAQDDHGNVWYKFGGDYGDYPNNYNFCLDGLIYSDQTPGPGLKEYKQVIA 600

Query: 601  PVKIHARDLTRGELKVENKLWFTTLDDYTLHAEVRAEGETLATQQIKLRDVAPNSEAPLQ 660
            PVKIHARDLTRGELKVENKLWFTTLDDYTLHAEVRAEGETLATQQIKLRDVAPNSEAPLQ
Sbjct: 601  PVKIHARDLTRGELKVENKLWFTTLDDYTLHAEVRAEGETLATQQIKLRDVAPNSEAPLQ 660

Query: 661  ITLPQLDAREAFLNITVTKDSRTRYSEAGHPIATYQFPLKENTAQPVPFAPNNARPLTLE 720
            ITLPQLDAREAFLNITVTKDSRTRYSEAGHPIATYQFPLKENTAQPVPFAPNNARPLTLE
Sbjct: 661  ITLPQLDAREAFLNITVTKDSRTRYSEAGHPIATYQFPLKENTAQPVPFAPNNARPLTLE 720

Query: 721  DDRLSCTVRGYNFAITFSKMSGKPTSWQVNGESLLTREPKINFFKPMIDNHKQEYEGLWQ 780
            DDRLSCTVRGYNFAITFSKMSGKPTSWQVNGESLLTREPKINFFKPMIDNHKQEYEGLWQ
Sbjct: 721  DDRLSCTVRGYNFAITFSKMSGKPTSWQVNGESLLTREPKINFFKPMIDNHKQEYEGLWQ 780

Query: 781  PNHLQIMQEHLRDFAVEQSDGEVLIISRTVIAPPVFDFGMRCTYIWRIAADGQVNVALSG 840
            PNHLQIMQEHLRDFAVEQSDGEVLIISRTVIAPPVFDFGMRCTYIWRIAADGQVNVALSG
Sbjct: 781  PNHLQIMQEHLRDFAVEQSDGEVLIISRTVIAPPVFDFGMRCTYIWRIAADGQVNVALSG 840

Query: 841  ERYGDYPHIIPCIGFTMGINGEYDQVAYYGRGPGENYADSQQANIIDIWRSTVDAMFENY 900
            ERYGDYPHIIPCIGFTMGINGEYDQVAYYGRGPGENYADSQQANIIDIWRSTVDAMFENY
Sbjct: 841  ERYGDYPHIIPCIGFTMGINGEYDQVAYYGRGPGENYADSQQANIIDIWRSTVDAMFENY 900

Query: 901  PFPQNNGNRQHVRWTALTNRHGNGLLVVPQRPINFSAWHYTQENIHAAQHCNELQRSDDI 960
            PFPQNNGNRQHVRWTALTNRHGNGLLVVPQRPINFSAWHYTQENIHAAQHCNELQRSDDI
Sbjct: 901  PFPQNNGNRQHVRWTALTNRHGNGLLVVPQRPINFSAWHYTQENIHAAQHCNELQRSDDI 960

Query: 961  TLNLDHQLLGLGSNSWGSEVLDSWRVWFRDFSYGFTLLPVSGGEATAQSLASYEFGAGFF 1020
            TLNLDHQLLGLGSNSWGSEVLDSWRVWFRDFSYGFTLLPVSGGEATAQSLASYEFGAGFF
Sbjct: 961  TLNLDHQLLGLGSNSWGSEVLDSWRVWFRDFSYGFTLLPVSGGEATAQSLASYEFGAGFF 1020

Query: 1021 STNLHSENKQ 1030
            STNLHSENKQ
Sbjct: 1021 STNLHSENKQ 1030


Lambda     K      H
   0.320    0.137    0.433 

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: 4176
Number of extensions: 185
Number of successful extensions: 1
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: 1030
Length of database: 1030
Length adjustment: 45
Effective length of query: 985
Effective length of database: 985
Effective search space:   970225
Effective search space used:   970225
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.

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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