GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Amantichitinum ursilacus IGB-41

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_053937127.1 WG78_RS07200 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::Q9I6J2
         (456 letters)



>NCBI__GCF_001294205.1:WP_053937127.1
          Length = 447

 Score =  261 bits (667), Expect = 3e-74
 Identities = 149/429 (34%), Positives = 234/429 (54%), Gaps = 16/429 (3%)

Query: 24  PFTDYKQLNEKGA-RIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQM 82
           PFT  +   +  A R +  A+G Y  ++ G  + D ++GLWC  +G+G   +V+   RQ 
Sbjct: 18  PFTGNRAFKDNPAQRTLVSAKGAYYQNAAGQTLFDCLSGLWCTPLGHGHPAIVETLKRQA 77

Query: 83  RELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKG 142
             L  Y   FQ ++P  + LA+ IA+ AP G++HVFFT SGSE+ DT L++   Y   +G
Sbjct: 78  ETLD-YGTGFQFSNPQTLRLAERIAERAPAGLDHVFFTNSGSESIDTALKIAIGYHRLRG 136

Query: 143 QPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQ-GDFPIPGIVHIAQPYWYGEGG-DMSP 200
           +  +  +IGR  GYHG    GVS+GGM A  +      + G+ H+   +   E       
Sbjct: 137 EATRFRMIGRERGYHGVGFGGVSVGGMVANRKMFAPLMLNGVDHLPHTHNLSEMAFSRGQ 196

Query: 201 DEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFI 260
            ++G   A++LEK +      ++AA I EP+ G+ GV+ PP+ Y  ++R+I  ++ IL I
Sbjct: 197 PKWGAHLADELEKLVALHDASSIAAVIVEPMAGSTGVLAPPEGYLQRLRDICTRHGILLI 256

Query: 261 ADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG--- 317
            DEVICGFGR G+WF +  +G  PD++  AK +T+G +P+GGV+VR EI +    G    
Sbjct: 257 FDEVICGFGRLGDWFAASRFGVTPDMICFAKTITNGVVPLGGVIVRPEIYQAFMTGPAHA 316

Query: 318 -EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEAR 376
            EF HG+TYSGHP+AAAV    + ++  E  ++  +A   P L+     L D   + + R
Sbjct: 317 VEFMHGYTYSGHPLAAAVGNTVLDLIDSEGHLQHARA-LEPVLENAVHALRDESSITDIR 375

Query: 377 GVGMVAALELVKNKKTRERFTDKGV-GMLCREHCFRNGLIMRAVGDTMIISPPLVIDPSQ 435
            +G+ AA++L             G+ G    E   + G + R  GDT+ + PP +  P++
Sbjct: 376 NMGLAAAVDLAPIP------GQPGLRGYRVFEAGLQKGHLFRVTGDTVAMGPPFIAQPAE 429

Query: 436 IDELITLAR 444
           I+ +    R
Sbjct: 430 IETMTACLR 438


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: 25
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: 447
Length adjustment: 33
Effective length of query: 423
Effective length of database: 414
Effective search space:   175122
Effective search space used:   175122
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