GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Desulfovibrio vulgaris Miyazaki F

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate 8499751 DvMF_0516 aminotransferase class-III (RefSeq)

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__Miya:8499751 DvMF_0516 aminotransferase
           class-III (RefSeq)
          Length = 459

 Score =  226 bits (577), Expect = 9e-64
 Identities = 143/440 (32%), Positives = 220/440 (50%), Gaps = 19/440 (4%)

Query: 20  HHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAG-LWCVNVGYGREELVQAA 78
           HHL     ++    KG  I+ + EG+ + D  G + LDA +G +WCVNVGYGRE + +A 
Sbjct: 22  HHL---VQHQAFAGKGPMIVVEGEGLTLRDINGKEYLDATSGGVWCVNVGYGRERIARAV 78

Query: 79  TRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYW 138
             QM+ +P+Y       + P +E A+ +    P G+   + + SGSEAN+   +MVR   
Sbjct: 79  YEQMKAMPYYAA--TAGNIPYIEFAQKLLAHMP-GLTRAYLSNSGSEANEKAYKMVRSLA 135

Query: 139 ATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDM 198
              G P KK ++ R   YHG+T+  +S  G     E     +PG V       Y    + 
Sbjct: 136 HLSGNPAKKKILFRARDYHGTTLGALSSTGQAERKEWFGPLVPGFVEFPHACCYRCAFNK 195

Query: 199 SPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDIL 258
           +     +  A  +E+ I + G E V   I EPI   GGVI P   Y+  + +I  ++ +L
Sbjct: 196 TYPGCDIDCARAVERIIEQEGPETVGGLIVEPITAGGGVIPPVAEYYTVLADICRRHGVL 255

Query: 259 FIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEV-LNQGG 317
            I DEV+CG GRTG  FG Q+YG  PD++ +AKG+ S Y+P+      +E+ +  LN   
Sbjct: 256 LIMDEVVCGMGRTGTMFGYQHYGVTPDIVTMAKGVASAYMPISVTATTEEVFKAFLNDPA 315

Query: 318 E----FYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVG 373
           +    F    TY G     + ALEN+ I+ EEK+++ V A    YL    +EL D P VG
Sbjct: 316 DKMAYFRDISTYGGCAAGCSAALENMAIIEEEKLLDNVNA-MGDYLLAGLKELGDLPYVG 374

Query: 374 EARGVGMVAALELVKNKKTRERFTDKGVGMLCREHCFRNGLIMR------AVGDTMIISP 427
           + RG G++  +ELV++K  ++   +  V  +  E      L+ R         + + I+P
Sbjct: 375 DVRGKGLLCGIELVQDKAGKKPMAEGKVIQVVGEMAANAVLVGRTNRSLPGFNNIINIAP 434

Query: 428 PLVIDPSQIDELITLARKCL 447
             V+    ID ++   R  L
Sbjct: 435 AYVVTRDNIDVILRTLRAAL 454


Lambda     K      H
   0.320    0.138    0.425 

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: 563
Number of extensions: 35
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: 456
Length of database: 459
Length adjustment: 33
Effective length of query: 423
Effective length of database: 426
Effective search space:   180198
Effective search space used:   180198
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: 51 (24.3 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