Alignments for a candidate for glnA in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Bacteroides thetaiotaomicron VPI-5482

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate 353865 BT4339 glutamine synthetase (NCBI ptt file)

Query= BRENDA::Q5LGP1
         (729 letters)



>FitnessBrowser__Btheta:353865
          Length = 729

 Score = 1373 bits (3555), Expect = 0.0
 Identities = 676/729 (92%), Positives = 705/729 (96%)

Query: 1   MSKMRFFALQELSNRKPLEITTPSNKLSDYYASHVFDRKKMQEYLPKEAYKAVVDATEKG 60
           MSKMRF+ALQELSNRKPLE+T PSNKLSDYY SHVFDRKKMQEYLPKEAYKAV DA EKG
Sbjct: 1   MSKMRFYALQELSNRKPLEVTAPSNKLSDYYGSHVFDRKKMQEYLPKEAYKAVTDAIEKG 60

Query: 61  TPISREMADLIANGMKSWAKSLNVTHYTHWFQPLTDGTAEKHDGFIEFGEDGEVIERFSG 120
           TPISRE+ADLIANGMKSWAKSLNVTHYTHWFQPLTDGTAEKHDGFIEFGEDG VIERFSG
Sbjct: 61  TPISREIADLIANGMKSWAKSLNVTHYTHWFQPLTDGTAEKHDGFIEFGEDGGVIERFSG 120

Query: 121 KLLIQQEPDASSFPNGGIRNTFEARGYTAWDVSSPAFVVDTTLCIPTIFISYTGEALDYK 180
           KLLIQQEPDASSFPNGGIRNTFEARGYTAWDVSSPAFVVDTTLCIPTIFISYTGEALDYK
Sbjct: 121 KLLIQQEPDASSFPNGGIRNTFEARGYTAWDVSSPAFVVDTTLCIPTIFISYTGEALDYK 180

Query: 181 TPLLKALAAVDKAATEVCQLFDKNITRVFTNLGWEQEYFLVDTSLYNARPDLRLTGRTLM 240
           TPLLKALAAVDKAATEVCQLFDKN+TRVFTNLGWEQEYFLVD+SLYNARPDL LTGRTLM
Sbjct: 181 TPLLKALAAVDKAATEVCQLFDKNVTRVFTNLGWEQEYFLVDSSLYNARPDLCLTGRTLM 240

Query: 241 GHSSAKDQQLEDHYFGSIPPRVTAFMKELEIECHKLGIPVKTRHNEVAPNQFELAPIFEN 300
           GHSSAKDQQLEDHYFGSIPPRVTAFMKELEIECHKLGIP KTRHNEVAPNQFELAPIFEN
Sbjct: 241 GHSSAKDQQLEDHYFGSIPPRVTAFMKELEIECHKLGIPAKTRHNEVAPNQFELAPIFEN 300

Query: 301 CNLANDHNQLVMDLMKRIARKHHFAVLFHEKPYNGVNGSGKHNNWSLCTDTGINLFAPGK 360
           CNLANDHNQLVMDLMKRIARKHHF VL HEKPY+ VNGSGKHNNWSLCTDTGINLFAPGK
Sbjct: 301 CNLANDHNQLVMDLMKRIARKHHFNVLLHEKPYSSVNGSGKHNNWSLCTDTGINLFAPGK 360

Query: 361 NPKGNMLFLTFLVNVLMMVHKNQDLLRASIMSAGNSHRLGANEAPPAILSIFLGSQLSAT 420
           NPKGNMLFLTFLVNVLMMV+KNQDLLRASIMSA NS+RLGANEAPPAILS FLGSQLSAT
Sbjct: 361 NPKGNMLFLTFLVNVLMMVYKNQDLLRASIMSASNSYRLGANEAPPAILSCFLGSQLSAT 420

Query: 421 LDEIVRQVTNSKMTPEEKTTLKLGIGRIPEILLDTTDRNRTSPFAFTGNRFEFRAAGSSA 480
           LDEIVRQV N KMTPEEKTTLKLGIGRIPEILLDTTDRNRTSPFAFTGNRFEFRAAGSS+
Sbjct: 421 LDEIVRQVGNEKMTPEEKTTLKLGIGRIPEILLDTTDRNRTSPFAFTGNRFEFRAAGSSS 480

Query: 481 NCAAAMIAINAAMANQLNEFKASVDKLMEEGIGKDEAIFRILKENIIASEPIRFEGDGYS 540
           NCAAAMIAINAAMANQLNEF+ASV+KLMEEG+GKDEAIFR+LKE IIASE IRFEGDGYS
Sbjct: 481 NCAAAMIAINAAMANQLNEFRASVEKLMEEGVGKDEAIFRLLKETIIASEAIRFEGDGYS 540

Query: 541 EEWKQEAARRGLTNICHVPEALMHYMDNQSRAVLIGERIFNETELACRLEVELEKYTMKV 600
           EEW+QEAARRGLTNICHVPEALMHY+DNQS++VLIGERIFNETEL  RLEVELEKYTMKV
Sbjct: 541 EEWRQEAARRGLTNICHVPEALMHYVDNQSKSVLIGERIFNETELNSRLEVELEKYTMKV 600

Query: 601 QIESRVLGDLAINHIVPIAVSYQNRLLENLCRMKEIFSEEEYEVMSADRKELIKEISHRV 660
           QIE RVLGDLAINHIVP AV+YQNRLLENLC+MKEIFS EEYEV+SADRKELI+EISHRV
Sbjct: 601 QIEGRVLGDLAINHIVPTAVTYQNRLLENLCKMKEIFSPEEYEVLSADRKELIREISHRV 660

Query: 661 SAIKVLVRDMTEARKVANHKENFKEKAFAYEETVRPYLESIRDHIDHLEMEIDDEIWPLP 720
           ++IKVLVR+MTEARKVANHK+N+KE+AF YEE VRPYL+ IRDHIDHLEME+DDEIWPLP
Sbjct: 661 TSIKVLVREMTEARKVANHKDNYKERAFEYEEKVRPYLDKIRDHIDHLEMEVDDEIWPLP 720

Query: 721 KYRELLFTK 729
           KYRELLFTK
Sbjct: 721 KYRELLFTK 729


Lambda     K      H
   0.319    0.134    0.390 

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: 1630
Number of extensions: 39
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: 729
Length of database: 729
Length adjustment: 40
Effective length of query: 689
Effective length of database: 689
Effective search space:   474721
Effective search space used:   474721
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 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis