Alignments for a candidate for glnP in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

GapMind for catabolism of small carbon sources

Alignments for a candidate for glnP in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Align Glutamine ABC transporter permease and substrate binding protein protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized)
to candidate WP_012412537.1 NPUN_RS32115 ABC transporter permease subunit

Query= TCDB::Q9CES5
         (714 letters)



>NCBI__GCF_000020025.1:WP_012412537.1
          Length = 496

 Score =  211 bits (537), Expect = 7e-59
 Identities = 141/465 (30%), Positives = 236/465 (50%), Gaps = 17/465 (3%)

Query: 259 KDVYTIASDNSFAPFEF---QNDDKQFTGIDVDLLNAIAKNQGFKLKWNFIGFQAAVDSV 315
           KD  T+ +   + P+EF   +  D+Q  G D+D+   +A+  GFKL+     F   + ++
Sbjct: 37  KDTLTMITSPDYPPYEFYDTKGGDRQIVGFDIDIAKTLAEKLGFKLQIMESDFNGLIPAL 96

Query: 316 QSGHADGMMSGMSITDARKQVFDYGSPYYSSNLTIATSSTDDSIKSWKDLKGKTLGAKNG 375
           Q+  AD +M+GM+ T  R++  D+   YY +  TI       ++K  +DL GK LG + G
Sbjct: 97  QANRADFVMAGMTPTPERQKNIDFSIIYYEAKDTIVAPK-GSNLKQPQDLLGKKLGVQLG 155

Query: 376 TASFDYLNAHAKEY-GYTVKTFTDATTMYSSLNNGSINALMDDEPVIKYAIKQGQKFATP 434
           T         +++  G  +K       +   + +G I+A + ++ V K   +        
Sbjct: 156 TIQEQNARKISQKVAGIQLKQLNKVPEVVQEIKSGRIDAAIVEDTVAKGFAQANPDLEFN 215

Query: 435 IKPIPDGQYGFAVKKGSNPELIEMFNNGLANLRANGEYDKIIDKYLESD--AKTIQSSAK 492
             P  +   G A+        +E FN  L  ++ +G   K++ K+   +  A ++ S+  
Sbjct: 216 TIPSEEAS-GSAIAFPKGSSFVEPFNKVLQQMKDDGTLAKLVTKWFSQNTAANSVSSTPA 274

Query: 493 E---NTFFGILQNNWEQIGRGLLVTLELAILSFILAMIVGIIFGLFSVAPSKILRTIARI 549
           +   N  F  +  +   I RG+ +TL   +LS  L +I G I  L  +   K L  +A  
Sbjct: 275 KGGLNLDFTRILPDIPFILRGIPLTLLFTLLSVTLGLIWGTILSLLKILGIKPLTWVANA 334

Query: 550 YVDLNRSIPLLVLTIFIFYGIPNLLQIITGHQSPLNEFTAGVIALTLNSSAYIAEIVRSG 609
           Y  + R  PLL+    ++Y  P L    TG+   ++   AGV+  TLNS AY++E +R G
Sbjct: 335 YTSVFRGTPLLLQLALVYYATPQL----TGYD--ISALEAGVLTFTLNSGAYMSETIRGG 388

Query: 610 VQAVPSGQMEASRSLGVTYLTSMRKVILPQAIKITIPSLINQFIITLKDTTLVSVIGLVE 669
           +QAV  GQ EA+ S+GV Y   M  VILPQA+K  +P+L+N+ I  LKD+ LVS IG+VE
Sbjct: 389 IQAVDKGQSEAAMSMGVPYWLMMWDVILPQALKNILPALVNETIGLLKDSALVSTIGVVE 448

Query: 670 LLQTGQIIVARNFQAFRVYGLIGLVYMIVLLFLMWIGRRVEKRMK 714
           +L++ QI+ A  +  F      GL+Y ++++ +      +EKR++
Sbjct: 449 ILRSAQIVGANKYIYFEPLLFAGLIYYVLVMGMTLGASALEKRLR 493



 Score =  105 bits (262), Expect = 5e-27
 Identities = 74/233 (31%), Positives = 117/233 (50%), Gaps = 6/233 (2%)

Query: 19  LVAPSVKAETTVKIASDSSYAPFEF---QNGQKKWVGIDVDIMQEVAKINDWKLEMSYPG 75
           L A S   + T+ + +   Y P+EF   + G ++ VG D+DI + +A+   +KL++    
Sbjct: 29  LKAVSSLGKDTLTMITSPDYPPYEFYDTKGGDRQIVGFDIDIAKTLAEKLGFKLQIMESD 88

Query: 76  FDAALQNLKAGQVDGIIAGMTITDERKETFDFSNPYYTSALTIATTKDSKLSDYSDLKGK 135
           F+  +  L+A + D ++AGMT T ER++  DFS  YY +  TI   K S L    DL GK
Sbjct: 89  FNGLIPALQANRADFVMAGMTPTPERQKNIDFSIIYYEAKDTIVAPKGSNLKQPQDLLGK 148

Query: 136 AVGAKNGT-AAQTWLQENQKKYGYTIKTYSDGVHMFAALSSGNIAGAMDEVPVISYAMKQ 194
            +G + GT   Q   + +QK  G  +K  +    +   + SG I  A+ E  V     + 
Sbjct: 149 KLGVQLGTIQEQNARKISQKVAGIQLKQLNKVPEVVQEIKSGRIDAAIVEDTVAKGFAQA 208

Query: 195 GQDLAMNFPSISLPGGYGFAVMKGKNSTLVDGFNKALAEMKSNGDYDKILKKY 247
             DL  N  +I      G A+   K S+ V+ FNK L +MK +G   K++ K+
Sbjct: 209 NPDLEFN--TIPSEEASGSAIAFPKGSSFVEPFNKVLQQMKDDGTLAKLVTKW 259


Lambda     K      H
   0.318    0.134    0.380 

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: 766
Number of extensions: 46
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 714
Length of database: 496
Length adjustment: 37
Effective length of query: 677
Effective length of database: 459
Effective search space:   310743
Effective search space used:   310743
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
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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 2024 update 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