GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Caulobacter crescentus NA1000

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate CCNA_03233 CCNA_03233 Acetyl ornithine aminotransferase

Query= BRENDA::Q9I6J2
         (456 letters)



>FitnessBrowser__Caulo:CCNA_03233
          Length = 467

 Score =  524 bits (1350), Expect = e-153
 Identities = 253/453 (55%), Positives = 321/453 (70%), Gaps = 4/453 (0%)

Query: 1   MNSQITNAKTREWQALSRDHHLPPFTDYKQLNEKG-ARIITKAEGVYIWDSEGNKILDAM 59
           MN+ I N    E + L   HHLP   D+K + E G +RI+T+A+G YI D +G++ILD M
Sbjct: 1   MNAPIRNHDVAELKRLDLAHHLPAQADHKVIAELGGSRIVTRADGCYITDGDGHRILDGM 60

Query: 60  AGLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFF 119
           AGLWCVNVGYGR+EL  AA  QM ELP+YN FF+TA PP V+LA  IA+     + HVFF
Sbjct: 61  AGLWCVNVGYGRKELADAAYEQMLELPYYNTFFKTATPPTVKLAAKIAEKMGGHLTHVFF 120

Query: 120 TGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFP 179
             SGSEANDTV R+VRHYW  KGQP + V I RWN YHGSTVAGVSLGGMK +H QGD P
Sbjct: 121 NSSGSEANDTVFRLVRHYWKLKGQPNRTVFISRWNAYHGSTVAGVSLGGMKHMHVQGDLP 180

Query: 180 IPGIVHIAQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIV 239
           IPG+ H+ QPY +GEG    P  F   A +++E KILEVG ENVAAFI EP+QGAGGVI+
Sbjct: 181 IPGVEHVMQPYPFGEGFGEDPAAFRDRAVKEIEDKILEVGPENVAAFIGEPVQGAGGVII 240

Query: 240 PPDTYWPKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIP 299
           PPD YWP +  +  KY IL + DEVICGFGR G+WFG Q+YG  PDL+ +AKGL+SGY+P
Sbjct: 241 PPDGYWPAVEAVCRKYGILLVCDEVICGFGRLGQWFGHQHYGIKPDLIAMAKGLSSGYLP 300

Query: 300 MGGVVVRDEIV-EVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPY 358
           +  V V D IV E+  +GG+F HGFTYSGHP  AAVAL+NI I+  E +I + + +T PY
Sbjct: 301 ISAVGVADHIVAELREKGGDFIHGFTYSGHPTCAAVALKNIEIIEREDLITRTREDTGPY 360

Query: 359 LQKRWQELADHPLVGEARGVGMVAALELVKNKKTRERFTDK--GVGMLCREHCFRNGLIM 416
           L K    L DHPLVGE R +G++ A+E+V+ K T  RF DK    G + R+ C RNGL++
Sbjct: 361 LAKALARLNDHPLVGETRSLGLIGAVEIVREKGTNHRFLDKEGEAGPIVRDICIRNGLMV 420

Query: 417 RAVGDTMIISPPLVIDPSQIDELITLARKCLDQ 449
           RA+ D+++  PPL++  ++IDEL+ +  K L +
Sbjct: 421 RAIRDSIVCCPPLIVSHAEIDELVGIIEKSLTE 453


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: 711
Number of extensions: 39
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: 467
Length adjustment: 33
Effective length of query: 423
Effective length of database: 434
Effective search space:   183582
Effective search space used:   183582
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:

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