GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Pseudomonas fluorescens GW456-L13

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate PfGW456L13_2414 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2414 Omega-amino
           acid--pyruvate aminotransferase (EC 2.6.1.18)
          Length = 472

 Score =  328 bits (841), Expect = 2e-94
 Identities = 169/443 (38%), Positives = 268/443 (60%), Gaps = 7/443 (1%)

Query: 20  HHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAAT 79
           HH+  +  + +  E+G+  I   +G YI+D++GN+ LDA+ G+WC N+G GREE+ +A  
Sbjct: 24  HHMHGYHVFDEHAEQGSLNIVAGDGAYIYDTQGNRFLDAVGGMWCTNIGLGREEMAEAIA 83

Query: 80  RQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWA 139
            Q+R+L + N F   ++   +EL + +A +AP  ++HVF T  GS A DT  R++++Y  
Sbjct: 84  DQVRQLAYSNPFSDMSNNVAIELCEKLASLAPGDLDHVFLTTGGSTAVDTAYRLIQYYQN 143

Query: 140 TKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALH-EQGDFPIPGIVHIAQPYWYGEGGDM 198
            +G+P+KK +I R+N YHGST   +S+G   A    + D+  P I H++ P  Y     M
Sbjct: 144 CRGKPEKKHIIARFNAYHGSTTLTMSIGNKAADRVPEFDYTNPLIHHVSNPNPYRAPDGM 203

Query: 199 SPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDIL 258
              +F  +  ++ E KIL +G + VA F AEPI G+GGVI+PP  Y  ++ ++  +YDIL
Sbjct: 204 DEAQFLEFLVKEFEDKILSIGADKVAGFFAEPIMGSGGVIIPPRGYLKRMWDVCQRYDIL 263

Query: 259 FIADEVICGFGRTGEWFGS-QYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG 317
           F+ADEV+  FGR G++F S + +   PD++  AKGLTS Y+P+G  +  + I +V+ + G
Sbjct: 264 FVADEVVTSFGRLGKFFASYEVFDVQPDIITTAKGLTSAYLPLGACIFSERIWKVIAEPG 323

Query: 318 E---FYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGE 374
           +   F HGFTYSGHPV    AL+NI I+  E ++  V    A YL++R   L D PLVG+
Sbjct: 324 KGRCFTHGFTYSGHPVCCTAALKNIEIIERENLLAHVDTVGA-YLEERLATLRDLPLVGD 382

Query: 375 ARGVGMVAALELVKNKKTRERFTDK-GVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDP 433
            R   ++A +E V +K+T+  F D+  +G          GL++R +    ++SPPL++  
Sbjct: 383 VRCQKLMACVEFVADKRTKALFPDEINIGEKIHVRAQARGLLVRPIMHLNVMSPPLILTS 442

Query: 434 SQIDELITLARKCLDQTAAAVLA 456
            Q+DE++   R C+ + AA + A
Sbjct: 443 VQVDEIVETLRTCILEVAAELEA 465


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: 550
Number of extensions: 27
Number of successful extensions: 6
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: 472
Length adjustment: 33
Effective length of query: 423
Effective length of database: 439
Effective search space:   185697
Effective search space used:   185697
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