GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ARO8 in Desulfovibrio vulgaris Miyazaki F

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate 8502295 DvMF_3003 putative transcriptional regulator, GntR family (RefSeq)

Query= SwissProt::H3ZPL1
         (417 letters)



>lcl|FitnessBrowser__Miya:8502295 DvMF_3003 putative transcriptional
           regulator, GntR family (RefSeq)
          Length = 394

 Score =  314 bits (804), Expect = 3e-90
 Identities = 162/389 (41%), Positives = 244/389 (62%), Gaps = 16/389 (4%)

Query: 32  SEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQALQYGTTKGFTPL 91
           S IRE+LK+    D+IS AGGLP P +FPV+ +      VLE+   +ALQY TT+GF PL
Sbjct: 13  SYIREILKVTAQPDIISFAGGLPHPASFPVDAVASAAASVLEEAGPEALQYTTTEGFPPL 72

Query: 92  RLALAEWMRERYD---IPISKVDIMTTSGSQQALDLIGRVFINPGDIIVVEAPTYLAALQ 148
           R    +W+ +RY    I +S  DI+ T+GSQQALDL+ +  I+ G  +V+E P YL A+Q
Sbjct: 73  R----QWIADRYKRQGINVSPDDILITTGSQQALDLVAKACIDRGGRVVMERPGYLGAIQ 128

Query: 149 AFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNPAGVTMNEKRR 208
            F  + P+FV +PL   G++ D L        K     ++ Y +P+FQNP+G+T +E+ R
Sbjct: 129 CFSVFGPDFVTVPLTPRGVDTDALR-------KAATGAQVFYAVPSFQNPSGITYDEQTR 181

Query: 209 KRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSKILAPGFRIGW 268
           + + E+ ++   ++VEDNPYGELR+ G+ + P++A+ +   V+ LG+FSK+++PG R+GW
Sbjct: 182 REVAEIMAETGCLMVEDNPYGELRFMGQHLPPVRAYMQAPSVL-LGSFSKVVSPGLRLGW 240

Query: 269 IAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEFYKPRRDAMLKA 328
           + A    +  +  AKQ+ DL T  F+Q I  +Y+    +DKHI  I   Y  +RDAM++A
Sbjct: 241 VCAPQEVLNPMITAKQASDLHTPGFTQRILHRYLMDNDVDKHIASIRARYGAQRDAMVQA 300

Query: 329 LEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTM 388
           +    P+ V  T+PEGGMF+W TLPEGI  + +  KA+ + VA+VPG  F+   +  +T 
Sbjct: 301 IRRHFPEDVACTEPEGGMFLWCTLPEGISAEALFHKAIERKVAFVPGRPFYVD-ETDDTF 359

Query: 389 RLNFTYVPEEKIREGIKRLAETIKEEMKK 417
           RLNF+    E I EGI RL + ++E + K
Sbjct: 360 RLNFSNSSPELIEEGIARLGQCLREYLGK 388


Lambda     K      H
   0.318    0.137    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: 459
Number of extensions: 24
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: 417
Length of database: 394
Length adjustment: 31
Effective length of query: 386
Effective length of database: 363
Effective search space:   140118
Effective search space used:   140118
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: 50 (23.9 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