Alignments for a candidate for glnA in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Shewanella oneidensis MR-1

Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate 200446 SO1268 glutamine synthetase (NCBI ptt file)

Query= curated2:O27612
         (442 letters)



>FitnessBrowser__MR1:200446
          Length = 451

 Score =  188 bits (478), Expect = 3e-52
 Identities = 136/430 (31%), Positives = 201/430 (46%), Gaps = 35/430 (8%)

Query: 23  QFVDIHGK--PKNMAIPLVRPDQIEDIIKDGLLFDGSSVEGFVDINESDLVLKPDPDTFS 80
           +F+D  G   P+++ +  V  D ++D I   LL D           + D V  PD +   
Sbjct: 36  KFLDEKGMRLPESVLLQTVTGDFVDDDIYYSLLDDA----------DIDFVCVPDENAVF 85

Query: 81  TLPWRPEEKGVCRFICDIYWPDGKPFEGDPRYVLKRALDKYAHLGYEYNVGPEPEFFILD 140
            LPW  E     + I D Y   G P E  PR VLK+ L  Y   G+E  + PE EF++  
Sbjct: 86  MLPWTIE--ATAQVIHDCYDRMGNPIELSPRNVLKKVLSLYDEKGWEPVIAPEMEFYLTS 143

Query: 141 QDEDGNII----------PHDCGAYFDVEPVDQGTDFRRKLVMDLEALNFDVEVSHHEVA 190
           + +D ++           P      F ++  ++       +    E    D++   HE  
Sbjct: 144 RSDDHDLPLKPPIGRSGRPEAGRQSFSIDAANEYDPLFEDMYDWCEIQGLDIDTLIHEDG 203

Query: 191 PGQHEIDFKFDKALKTADAVITFKQAIKAIVDKIGYMVTFMPKPFFGENGSGMHCHQSLF 250
           P Q EI+F     L  AD V  FK+ ++    K     TFM KP   E GS MH HQS+ 
Sbjct: 204 PAQMEINFSHGNPLSLADQVFVFKRTLREAALKHNVCATFMAKPVTDEPGSAMHIHQSVI 263

Query: 251 --KDGENVFYDPD-TETQLSEEALYFIGGLLKHAPALTAVCAPTVNSYKRLVPGYEAPVY 307
             + G+N+F + D T++ L    L +I GL K+ P    + AP  NS++R +PG  APV 
Sbjct: 264 NKETGKNIFTNEDGTQSALF---LSYIAGLQKYIPEFLPLMAPNANSFRRFLPGTSAPVN 320

Query: 308 IAYGLKNRSTLIRIPASRGKGTRVELRMPDPSCNPYLAFAAMLEAGMNGIQNKIDPGEPT 367
           + +G++NR+  +RIP S  +  R+E R+P    N YLAFAA L  G  G+   + P  P 
Sbjct: 321 LEWGIENRTCGLRIPESSPQNRRIENRIPGADANCYLAFAAGLLCGYIGMVEGLKPSTPV 380

Query: 368 EIDVYEKSMSELREMGIETLPSSLWEAYHALEEDDVIKGALGGHVYEKFMEIKHREWDDY 427
                +   +E R      LP +L EA  A+EE D  K  LG      F+ +K  E +++
Sbjct: 381 -----QGKANESRSNNPHCLPLTLEEALVAMEESDACKEYLGESFTTGFVAVKQAELENF 435

Query: 428 RVRVFKYELE 437
           R  V  +E E
Sbjct: 436 RRVVSSWERE 445


Lambda     K      H
   0.320    0.141    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: 540
Number of extensions: 31
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: 442
Length of database: 451
Length adjustment: 33
Effective length of query: 409
Effective length of database: 418
Effective search space:   170962
Effective search space used:   170962
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: 51 (24.3 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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