Alignments for a candidate for glnA in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Pedobacter sp. GW460-11-11-14-LB5

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate CA265_RS05180 CA265_RS05180 glutamine synthetase type III

Query= BRENDA::Q5LGP1
         (729 letters)



>FitnessBrowser__Pedo557:CA265_RS05180
          Length = 724

 Score =  841 bits (2172), Expect = 0.0
 Identities = 422/733 (57%), Positives = 541/733 (73%), Gaps = 13/733 (1%)

Query: 1   MSKMRFFALQELSNRKPLEITTPSNKLSDYYASHVFDRKKMQEYLPKEAYKAVVDATEKG 60
           M  +R  AL+E  NR   E+ +PS K+SD++ ++VFD++KM+++L K+ Y+ ++ +  +G
Sbjct: 1   MKSLRTIALKEAQNRISPEVKSPSAKISDFFGANVFDKRKMRDFLSKDVYEKLISSINQG 60

Query: 61  TPISREMADLIANGMKSWAKSLNVTHYTHWFQPLTDGTAEKHDGFIEFGEDGEVIERFSG 120
             I+ E A+ IA  MKSWA +   THYTHWFQPLT  TAEKHD F E   +G  IE+F+G
Sbjct: 61  ELINAEDANQIATAMKSWAMAAGATHYTHWFQPLTGTTAEKHDSFFEPSGEG-AIEKFAG 119

Query: 121 KLLIQQEPDASSFPNGGIRNTFEARGYTAWDVSSPAFVVDT----TLCIPTIFISYTGEA 176
             L+QQEPDASSFPNGGIRNTFEARGYTAWD SSPAF++++    TLCIPT+F+SYTGEA
Sbjct: 120 SALVQQEPDASSFPNGGIRNTFEARGYTAWDPSSPAFIMESKAGKTLCIPTVFVSYTGEA 179

Query: 177 LDYKTPLLKALAAVDKAATEVCQLFDKNITRVFTNLGWEQEYFLVDTSLYNARPDLRLTG 236
           LDYK PLLKALA++DKAA +VCQ FDK+IT+V  +LG EQEYFLVD SL+NARPDL LTG
Sbjct: 180 LDYKAPLLKALASLDKAAVDVCQYFDKSITKVNASLGIEQEYFLVDESLFNARPDLLLTG 239

Query: 237 RTLMGHSSAKDQQLEDHYFGSIPPRVTAFMKELEIECHKLGIPVKTRHNEVAPNQFELAP 296
           R L GH SAK QQLEDHYFGSIP RV ++M + E E  KLGIP+KTRHNEVAP+QFE AP
Sbjct: 240 RALFGHMSAKGQQLEDHYFGSIPERVFSYMVDFENEALKLGIPLKTRHNEVAPSQFECAP 299

Query: 297 IFENCNLANDHNQLVMDLMKRIARKHHFAVLFHEKPYNGVNGSGKHNNWSLCTDTGINLF 356
           I+E  NLA DHNQL+MDLM+++AR+HHF VL HEKPY G+NGSGKHNNWSL TDTG NL 
Sbjct: 300 IYEEINLAIDHNQLLMDLMEKVARRHHFRVLLHEKPYAGINGSGKHNNWSLITDTGKNLL 359

Query: 357 APGKNPKGNMLFLTFLVNVLMMVHKNQDLLRASIMSAGNSHRLGANEAPPAILSIFLGSQ 416
           APGK PK N++FL F VN +  V ++ DLLRASI S  N HRLGANEAPPAI+SIFLGSQ
Sbjct: 360 APGKTPKNNLMFLAFFVNTIKAVSEHADLLRASIASVSNDHRLGANEAPPAIISIFLGSQ 419

Query: 417 LSATLDEIVRQVTNSKMTPEEKTTLKLGIGRIPEILLDTTDRNRTSPFAFTGNRFEFRAA 476
           L+  LDEI     + K+  +E   L LGI +IP+ILLD TDRNRTSPFAFTGN+FE RA 
Sbjct: 420 LNDVLDEIEHSRISKKI--KEDNALWLGIPKIPQILLDNTDRNRTSPFAFTGNKFELRAV 477

Query: 477 GSSANCAAAMIAINAAMANQLNEFKASVDKLMEEGIGKDEAIFRILKENIIASEPIRFEG 536
           GSSAN +A M  +NA MA QL +FK  VDKL+++G  KD A+  ++K+ I  S+ IRFEG
Sbjct: 478 GSSANSSAPMTILNAIMAEQLVKFKVEVDKLIKKGDKKDIALLTVIKKYIKESKNIRFEG 537

Query: 537 DGYSEEWKQEAARRGLTNICHVPEALMHYMDNQSRAVLIGERIFNETELACRLEVELEKY 596
           +GYS+EW+ EAA RGL+NI   P+AL  Y+  +S  +     I++  E+  R E+ LE +
Sbjct: 538 NGYSQEWEDEAATRGLSNIKTTPKALDAYLTEKSAELFASTGIYSAREIHARHEIMLENF 597

Query: 597 TMKVQIESRVLGDLAINHIVPIAVSYQNRLLENLCRMKEIFSEEEYEVMSADRKELIKEI 656
             K+QIE+RV+G++A   I+P A++YQN L+EN+  +KE+       V S    +++K++
Sbjct: 598 YKKLQIEARVMGEVANTAIIPAAIAYQNSLIENVKGLKEL------GVDSKSSLDIVKKL 651

Query: 657 SHRVSAIKVLVRDMTEARKVANHKENFKEKAFAYEETVRPYLESIRDHIDHLEMEIDDEI 716
           S  +  +K  +  M E RK+ N  E+ +EKA AY+E V+ Y ++IR H D LE  +DD +
Sbjct: 652 SEHLDIVKTNIDAMLEERKLTNKIEDTREKAIAYDEKVKSYFDTIRYHADKLEQIVDDSV 711

Query: 717 WPLPKYRELLFTK 729
           WPLPK+RELLF K
Sbjct: 712 WPLPKFRELLFMK 724


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: 1240
Number of extensions: 45
Number of successful extensions: 5
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: 724
Length adjustment: 40
Effective length of query: 689
Effective length of database: 684
Effective search space:   471276
Effective search space used:   471276
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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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