GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ans in Marinobacter adhaerens HP15

Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate GFF1957 HP15_1914 asparagine synthase, glutamine-hydrolyzing

Query= BRENDA::P22106
         (554 letters)



>FitnessBrowser__Marino:GFF1957
          Length = 632

 Score =  147 bits (371), Expect = 1e-39
 Identities = 122/394 (30%), Positives = 188/394 (47%), Gaps = 56/394 (14%)

Query: 1   MCSIFGVFDIKT--DAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVN- 57
           MC I G     T  D  +    A  + + + HRGPD +G++   +  L H+RLSI+D++ 
Sbjct: 1   MCGIAGFLRTGTLPDREQHHLWAERMGQAIAHRGPDANGVHIDQDVALVHQRLSILDLSS 60

Query: 58  AGAQPLYNQQKTHVLAVNGEIYNHQALRAEYG-DRYQFQTGSDCEVILALYQEKGPEFLD 116
           AG QP+ +    +++  NGEIYN ++LR     D + F+T +D EV+LALY   G   L 
Sbjct: 61  AGNQPMASSCGRYIIVFNGEIYNFRSLREGLEQDGFSFKTQTDTEVLLALYARHGESCLR 120

Query: 117 DLQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKAL--VPVCR---- 170
            L GMFAFA++D++  +  IGRD LG  PLY   D  GQ +  SE+KAL   PV R    
Sbjct: 121 QLNGMFAFAIWDAKTKSLFIGRDRLGKKPLYY-TDTDGQFFFGSEIKALFATPVVRPALR 179

Query: 171 --TIKEF-------------------PAGSYLWSQDGEIRSYYHRDWFDYDAVKDNVTD- 208
              IK+F                   P G  +   +G I    + D          V+D 
Sbjct: 180 PDAIKDFFVYQYIPDPKTIYANVHKLPPGHCMEVCEGRISVRKYWDLSFRPVEGRTVSDI 239

Query: 209 KNELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWPQL 268
           K  L   ++++V+  ++SDVP G  LSGG+DSS +  +    +++ V             
Sbjct: 240 KAGLYDVIDEAVRLRMISDVPLGAFLSGGIDSSAVVGLMAGRSSQPVT------------ 287

Query: 269 HSFAVGLPGS--PDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETY--DVTTI 324
            +  +G       ++K A  VA    T HH   FTV+E    + D +  I  +  +    
Sbjct: 288 -TCTIGFDDEKFDEIKYADLVARQFKTDHHV--FTVKE---TVADNLVGISRFFDEPFAD 341

Query: 325 RASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGY 358
            +  P + +S+  +   + + L+G+G DE F GY
Sbjct: 342 PSFVPTFFVSQLARTQ-VTVALAGDGGDENFAGY 374



 Score = 41.2 bits (95), Expect = 1e-07
 Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 2/67 (2%)

Query: 388 RANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCGNGKMEKHILRECFEAYLPASVAW 447
           + ++   A  +E R P LD + ++ A  I    K+ GN K  KH+L+ECF   L   + +
Sbjct: 497 KVDRMSMANSLETRAPLLDYRVVEYAAGIPSALKLKGNCK--KHVLKECFSDLLDEDILY 554

Query: 448 RQKEQFS 454
           R+K  FS
Sbjct: 555 RKKMGFS 561


Lambda     K      H
   0.319    0.135    0.407 

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: 797
Number of extensions: 41
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: 554
Length of database: 632
Length adjustment: 37
Effective length of query: 517
Effective length of database: 595
Effective search space:   307615
Effective search space used:   307615
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: 53 (25.0 bits)

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

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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:

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:

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:

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:

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