GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xad in Shewanella sp. ANA-3

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate 7023120 Shewana3_0358 dihydroxy-acid dehydratase (RefSeq)

Query= reanno::pseudo5_N2C3_1:AO356_28760
         (594 letters)



>lcl|FitnessBrowser__ANA3:7023120 Shewana3_0358 dihydroxy-acid
           dehydratase (RefSeq)
          Length = 619

 Score =  210 bits (535), Expect = 1e-58
 Identities = 176/579 (30%), Positives = 268/579 (46%), Gaps = 81/579 (13%)

Query: 44  GRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAAL-- 101
           G+PII IA + +   P + H  ++   V   I +AGGI  EF    + +        +  
Sbjct: 33  GKPIIAIANSFTQFVPGHVHLKDMGSLVADAIEEAGGIAKEFNTIAVDDGIAMGHGGMLY 92

Query: 102 ---DRNLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGH 158
               R L    +  +++ +  D +V  + CDK TP  LMAA   ++P + +SGGPM  G 
Sbjct: 93  SLPSRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGK 152

Query: 159 HK--GELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEA 216
            K   +LI    V   A    A   +  E   ++  +A P+ G C+ M TA SMN L EA
Sbjct: 153 TKLSDKLIKLDLV--DAMVAAADSSVSDEDSAKIERSACPTCGSCSGMFTANSMNCLTEA 210

Query: 217 LGMSLPGCASIPAPYRERGQMAYATGKRICELVLQ-------DIRPSQIMTRQAFENAIA 269
           LG+SLPG  S+ A + +R ++    G+R+  L  +          P  I + +AFENA+A
Sbjct: 211 LGLSLPGNGSMLATHADRRELFLEAGRRVMALTKRYYEQDDASALPRNIASFKAFENAMA 270

Query: 270 VASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPA-GKYLGEGFHRAG 328
           +  A+G SSN   HL+A A+   V  ++DD  R+   VP L    P+  KY  E  HRAG
Sbjct: 271 LDIAMGGSSNTVLHLLAAAQEADVAFTMDDIDRMSRQVPHLCKVAPSTAKYHMEDVHRAG 330

Query: 329 GVPSVMHELQKAGRLHEDCATVSGRTIGEIVSSSLTSNADVIHPFDTPLK---------- 378
           GV  ++ EL +AG LH D   V+    G +   S+ +  DV+   D  +K          
Sbjct: 331 GVMGILGELDRAGLLHTDVPHVAADAGGNL--KSVLAKYDVMQTQDDKVKQFFMAGPAGI 388

Query: 379 --------------------------------HRAGFIVLSGNFFDS-AIMKMSVVGEAF 405
                                              G  VLSGN  D+  I+K + V E  
Sbjct: 389 PTTKAFSQDCRWPSLDDDRREGCIRSREFAFSQEGGLAVLSGNLADNGCIVKTAGVDE-- 446

Query: 406 RKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEV 465
                    +  +F   A V+E  +D  A I    +   +  ++VIR  G  G PG  E+
Sbjct: 447 ---------SNLTFIGSARVYESQDDAVAGILGGEVVAGD--VVVIRYEGPKGGPGMQEM 495

Query: 466 VNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVD 524
             + P + L  +G+  +   + DGR SG ++  SI ++SPEAA GG +AL++  DR+++D
Sbjct: 496 --LYPTSYLKSRGLGKACALITDGRFSGGTSGLSIGHVSPEAAAGGTIALIENGDRIEID 553

Query: 525 LNTRTVNLLIDDEEMARRRLEWTPNIPPSQTPWQELYRQ 563
           +  R++ L + D E+A RR       P +   W+ L RQ
Sbjct: 554 IPKRSIKLAVSDAELAARRETMLARGPMA---WKPLSRQ 589


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: 827
Number of extensions: 42
Number of successful extensions: 6
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: 594
Length of database: 619
Length adjustment: 37
Effective length of query: 557
Effective length of database: 582
Effective search space:   324174
Effective search space used:   324174
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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