Aligments for a candidate for lacZ in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments for a candidate for lacZ in Sinorhizobium meliloti 1021

Align Beta-galactosidase (EC 3.2.1.23) (characterized)
to candidate SM_b21655 SM_b21655 beta-galactosidase

Query= reanno::Smeli:SM_b21655
         (755 letters)



>FitnessBrowser__Smeli:SM_b21655
          Length = 755

 Score = 1547 bits (4005), Expect = 0.0
 Identities = 755/755 (100%), Positives = 755/755 (100%)

Query: 1   MMRSVTSFNDSWVFSEGFDAADAGTLRAGQPISLPHNAVELPFNYFDERCYQRAFTYQRV 60
           MMRSVTSFNDSWVFSEGFDAADAGTLRAGQPISLPHNAVELPFNYFDERCYQRAFTYQRV
Sbjct: 1   MMRSVTSFNDSWVFSEGFDAADAGTLRAGQPISLPHNAVELPFNYFDERCYQRAFTYQRV 60

Query: 61  LAWRPDFSGREVSLVFDAAMADAVVYLNGEEIVAHRDGYTPFEARLTDRLLEGDNLITVK 120
           LAWRPDFSGREVSLVFDAAMADAVVYLNGEEIVAHRDGYTPFEARLTDRLLEGDNLITVK
Sbjct: 61  LAWRPDFSGREVSLVFDAAMADAVVYLNGEEIVAHRDGYTPFEARLTDRLLEGDNLITVK 120

Query: 121 IDGSENPEIPPFGGRIDYLTYAGIYRDVWLKVTDPVSIANIKIETRDVLSDTKAVSLRCD 180
           IDGSENPEIPPFGGRIDYLTYAGIYRDVWLKVTDPVSIANIKIETRDVLSDTKAVSLRCD
Sbjct: 121 IDGSENPEIPPFGGRIDYLTYAGIYRDVWLKVTDPVSIANIKIETRDVLSDTKAVSLRCD 180

Query: 181 LSNPQGLSFSGTISALLKNAAGEVLAEVAGETTGQSLAFEMDGLKGLSLWDIDDPVLYVI 240
           LSNPQGLSFSGTISALLKNAAGEVLAEVAGETTGQSLAFEMDGLKGLSLWDIDDPVLYVI
Sbjct: 181 LSNPQGLSFSGTISALLKNAAGEVLAEVAGETTGQSLAFEMDGLKGLSLWDIDDPVLYVI 240

Query: 241 EVELRTGQGSDCFAAHFGFRTAEFTTEGFRLNGRPLKIRGLNRHQSFPYVGYAMGRTAQE 300
           EVELRTGQGSDCFAAHFGFRTAEFTTEGFRLNGRPLKIRGLNRHQSFPYVGYAMGRTAQE
Sbjct: 241 EVELRTGQGSDCFAAHFGFRTAEFTTEGFRLNGRPLKIRGLNRHQSFPYVGYAMGRTAQE 300

Query: 301 RDADIMKHRLHCNLVRTSHYPQSKWFLDHCDRIGLLVFEEIPGWQHIGGEEWKQEAIRNV 360
           RDADIMKHRLHCNLVRTSHYPQSKWFLDHCDRIGLLVFEEIPGWQHIGGEEWKQEAIRNV
Sbjct: 301 RDADIMKHRLHCNLVRTSHYPQSKWFLDHCDRIGLLVFEEIPGWQHIGGEEWKQEAIRNV 360

Query: 361 RRMIERDWNHPSIVIWGVRINESQDSHDFYAETNRLARELDPTRQTGGVRYITDSEFLED 420
           RRMIERDWNHPSIVIWGVRINESQDSHDFYAETNRLARELDPTRQTGGVRYITDSEFLED
Sbjct: 361 RRMIERDWNHPSIVIWGVRINESQDSHDFYAETNRLARELDPTRQTGGVRYITDSEFLED 420

Query: 421 VYTMNDFILGNEELPGANRPRTALRPQQECTGLPRKVPYLITEFGGHMYPTKIYDQEQRQ 480
           VYTMNDFILGNEELPGANRPRTALRPQQECTGLPRKVPYLITEFGGHMYPTKIYDQEQRQ
Sbjct: 421 VYTMNDFILGNEELPGANRPRTALRPQQECTGLPRKVPYLITEFGGHMYPTKIYDQEQRQ 480

Query: 481 AEHVRRHLEVLNAAYGDPGISGAIGWCMFDYNTHKDFGSGDRICYHGVMDMFREPKFAAY 540
           AEHVRRHLEVLNAAYGDPGISGAIGWCMFDYNTHKDFGSGDRICYHGVMDMFREPKFAAY
Sbjct: 481 AEHVRRHLEVLNAAYGDPGISGAIGWCMFDYNTHKDFGSGDRICYHGVMDMFREPKFAAY 540

Query: 541 VYASQCDPSEEIVMKPVTFWARGERNIGGVLPLIVLTNCDEIELKYGSLTKRVGPDRENF 600
           VYASQCDPSEEIVMKPVTFWARGERNIGGVLPLIVLTNCDEIELKYGSLTKRVGPDRENF
Sbjct: 541 VYASQCDPSEEIVMKPVTFWARGERNIGGVLPLIVLTNCDEIELKYGSLTKRVGPDRENF 600

Query: 601 PHLPHPPVVIDHRHFTKDELGVWGMKWESAEFTGFIAGKPVADLRMAADPVPTTLQVEAD 660
           PHLPHPPVVIDHRHFTKDELGVWGMKWESAEFTGFIAGKPVADLRMAADPVPTTLQVEAD
Sbjct: 601 PHLPHPPVVIDHRHFTKDELGVWGMKWESAEFTGFIAGKPVADLRMAADPVPTTLQVEAD 660

Query: 661 SKTLRAEGRDSVRLILRALDQAGNVQPFLNDAVDIEIHGPARLVGPARIVLQGGSAGFWL 720
           SKTLRAEGRDSVRLILRALDQAGNVQPFLNDAVDIEIHGPARLVGPARIVLQGGSAGFWL
Sbjct: 661 SKTLRAEGRDSVRLILRALDQAGNVQPFLNDAVDIEIHGPARLVGPARIVLQGGSAGFWL 720

Query: 721 ESTGAAGAIVVSVASSRLGAAKLDLVALADGAASA 755
           ESTGAAGAIVVSVASSRLGAAKLDLVALADGAASA
Sbjct: 721 ESTGAAGAIVVSVASSRLGAAKLDLVALADGAASA 755


Lambda     K      H
   0.321    0.138    0.427 

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: 1924
Number of extensions: 66
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: 755
Length of database: 755
Length adjustment: 40
Effective length of query: 715
Effective length of database: 715
Effective search space:   511225
Effective search space used:   511225
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: 55 (25.8 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, or view the source code.

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