GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Bacteroides thetaiotaomicron VPI-5482

Align Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate 351600 BT2072 aconitate hydratase (NCBI ptt file)

Query= SwissProt::Q937N8
         (869 letters)



>lcl|FitnessBrowser__Btheta:351600 BT2072 aconitate hydratase (NCBI
           ptt file)
          Length = 747

 Score =  207 bits (528), Expect = 1e-57
 Identities = 233/838 (27%), Positives = 358/838 (42%), Gaps = 153/838 (18%)

Query: 51  PATLTDSLL--------QLVGRKRDLDFPWF-PARVVCHDILGQTALVDLAGLRDAIADQ 101
           P TL + +L         L   KR  D+  F P RV   D   Q AL+            
Sbjct: 29  PLTLAEKILYAHLFNEGDLKNYKRGEDYVNFRPDRVAMQDATAQMALLQFM--------- 79

Query: 102 GGDPAKVNPVVPVQLIVDHSLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKN 161
             +  K    VP  +  DH +    G  +  A A       + NE+ + F+      +  
Sbjct: 80  --NAGKEKVAVPSTVHCDHLIQAYKGAKEDIATAT------KTNEEVYDFLRDVSSRY-G 130

Query: 162 VDVIPPGNGIMHQINLEKMSPVIHADNGVAYPD-TCVGTDSHTPHVDALGVIAIGVGGLE 220
           +    PG GI+HQ+ LE            A+P    VGTDSHTP+   LG++AIGVGG +
Sbjct: 131 IGFWKPGAGIIHQVVLENY----------AFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD 180

Query: 221 AENVMLGRASWMRLPDIVGVELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGA 280
           A +VM G    +++P I+GV LTGK     +  D++L L   L  +    + +E+ G G 
Sbjct: 181 AVDVMTGMEWELKMPRIIGVRLTGKLSGWTSPKDVILKLAGILTVKGGTNSIIEYFGPGT 240

Query: 281 SSLTLGDRATISNMAPEYGATAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWAD 340
           +SL+   +ATI NM  E GAT ++F  D +   YLR TGR D  ++L E  A    L AD
Sbjct: 241 ASLSATGKATICNMGAEVGATTSLFPFDGRMATYLRATGR-DRIVELAE--AVDCELRAD 297

Query: 341 SLKNAE----YERVLKFDLSSVVRNMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEG 396
                E    Y+RV+  DLS++   + GP  P    P S  AE+   V L+    +   G
Sbjct: 298 QQVTDEPEKYYDRVIDIDLSTLEPYINGPFTPDAATPISEFAEK---VLLNGYPRKMEVG 354

Query: 397 LMPDGAVIIAAITSCTNTSNPRNVIAAALLARNANARGLA-RKPWVKSSLAPGSKAVELY 455
           L          I SCTN+S  +++  AA LAR    + L+   P +   + PGS+ +   
Sbjct: 355 L----------IGSCTNSSY-QDLSRAASLARQVKEKNLSVASPLI---INPGSEQIRAT 400

Query: 456 LEEANLLPDLEKLGFGIVAFACTTCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNF--- 512
            E   ++ D  ++G  I+A AC  C G       + ++   D     + V S NRNF   
Sbjct: 401 AERDGMMDDFMQIGAVIMANACGPCIG-------QWKRHTDDPTRKNSIVTSFNRNFAKR 453

Query: 513 -DGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEID 571
            DG  + Y   AF+ASP L +A  IAG + F+  KD L  + DG+ V L +  P  +E+ 
Sbjct: 454 ADGNPNTY---AFVASPELTMALTIAGDLCFNPLKDRL-MNHDGEKVKLAE--PVGDEL- 506

Query: 572 AIVAKSVKPEQFRKVYEPMFAITAASGESVSP-----LYDWRPQSTYIRRP---PYWEGA 623
                            P+   T+ +   ++P       +  P S  ++     P W+G 
Sbjct: 507 -----------------PLRGFTSGNEGYITPGGTKTAINVNPASQRLQLLTPFPAWDG- 548

Query: 624 LAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAAGEYLARMGLPEEDFNSYATHRGD 683
               + +  +  L       TTDH+         S AG +L   G  E   ++      +
Sbjct: 549 ----QDILNMPLLIKAQGKCTTDHI---------SMAGPWLRFRGHLENISDNMLMGAVN 595

Query: 684 HLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEGKVVRMWEAIETYMDRKQPLIIIA 743
               +     N +  N    V G  K                      Y     P I++A
Sbjct: 596 AFNGETNNVWNRS-TNTYGTVSGTAK---------------------MYKSEGIPSIVVA 633

Query: 744 GADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTNLIGMGVLPLEFKPGVNRLTLGLD 803
             +YG+GSSR+ AA   R   V VI+A+ F RIH TNL   G+L L F    +      D
Sbjct: 634 EENYGEGSSREHAAMEPRFLNVRVILAKSFARIHETNLKKQGMLALTFADKAD-----YD 688

Query: 804 GTETYDVIG-----ERQPRATLTLVVNRKNGERVEVPVTCRLDSDEEVSIYEAGGVLH 856
             + +D++      +  P   LT+V++ ++G +          ++++++ + AG  L+
Sbjct: 689 KIQEHDLLSVIGLPDFAPGRNLTVVLHHEDGTKESFEAQ-HTYNEQQIAWFRAGSALN 745


Lambda     K      H
   0.318    0.135    0.398 

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: 1564
Number of extensions: 85
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: 869
Length of database: 747
Length adjustment: 41
Effective length of query: 828
Effective length of database: 706
Effective search space:   584568
Effective search space used:   584568
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: 56 (26.2 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 paper from 2022 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