GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Halioglobus japonicus S1-36

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_102106348.1 C0029_RS13280 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::Q9I6J2
         (456 letters)



>NCBI__GCF_002869505.1:WP_102106348.1
          Length = 454

 Score =  489 bits (1260), Expect = e-143
 Identities = 240/453 (52%), Positives = 319/453 (70%), Gaps = 6/453 (1%)

Query: 1   MNSQITNAKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMA 60
           MN Q   A T   + L + HHL PFTD+K     G R++++AE +YI+ +EG+K+LD M+
Sbjct: 1   MNMQ---ANTGNLKQLDQSHHLHPFTDFKDYATNGGRVMSRAEHIYIYTAEGHKMLDGMS 57

Query: 61  GLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFT 120
           GLWC N+GY +  +V A T Q+ +LP+YN FFQ ++ P +ELAKA+ D+ PE  NHVFFT
Sbjct: 58  GLWCCNLGYSQRSIVDAVTEQLGQLPYYNNFFQCSNQPAIELAKALVDITPERFNHVFFT 117

Query: 121 GSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPI 180
            SGSEANDT LR+V  Y+  +G+P+KK++I R N YHGST+A   LGGM  +HEQ +  I
Sbjct: 118 NSGSEANDTNLRLVSRYYQCQGRPEKKLIISRKNAYHGSTIAAACLGGMGPMHEQTN-GI 176

Query: 181 PGIVHIAQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVP 240
             + HI QP+W+  G D  P+EFG+  A QLE+KI E+GEENVAAFIAEP+QGAGGVI+P
Sbjct: 177 DYVHHIEQPHWFEVGPDEDPNEFGLRVARQLEEKIDELGEENVAAFIAEPVQGAGGVIIP 236

Query: 241 PDTYWPKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPM 300
           PD+YWP+++ I  + DIL IADEVICGFGRTG+W+GS+ YG  PDLM  AK +T+G+ P+
Sbjct: 237 PDSYWPEVQRICNERDILLIADEVICGFGRTGQWWGSETYGIEPDLMTFAKAVTNGFQPL 296

Query: 301 GGVVVRDEIVEV-LNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYL 359
           GGV+V D++ +V L   GEF HG TYSGHP AAA  L  + IL+E  +I    A  AP+ 
Sbjct: 297 GGVMVADKVADVLLAHEGEFAHGLTYSGHPAAAAAGLATLNILKEGNVIADAAANIAPHF 356

Query: 360 QKRWQELADHPLVGEARGVGMVAALELVKNKKTRERFTDKGVGML-CREHCFRNGLIMRA 418
           Q+R QELADH +VG+ RG GM AA+ELVK+K +RE    +  G L CR      GL++R 
Sbjct: 357 QRRLQELADHKIVGQVRGRGMFAAVELVKDKSSREPLAAESAGALFCRNTANELGLMVRQ 416

Query: 419 VGDTMIISPPLVIDPSQIDELITLARKCLDQTA 451
            G+ MI++PPL+   S+ID LI +  + LD TA
Sbjct: 417 TGNAMIMAPPLICSTSEIDSLIDMLGQALDVTA 449


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: 617
Number of extensions: 29
Number of successful extensions: 4
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: 454
Length adjustment: 33
Effective length of query: 423
Effective length of database: 421
Effective search space:   178083
Effective search space used:   178083
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 24 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:

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