GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Shewanella loihica PV-4

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate 5208066 Shew_0578 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

Query= reanno::Putida:PP_4108
         (416 letters)



>FitnessBrowser__PV4:5208066
          Length = 405

 Score =  194 bits (492), Expect = 5e-54
 Identities = 131/402 (32%), Positives = 202/402 (50%), Gaps = 36/402 (8%)

Query: 21  GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLAL 80
           G  + VWD +G  ++DF GGI V  LGHC+PA+V A++ Q  ++ H A N   + P LAL
Sbjct: 30  GEGSRVWDQEGNEFVDFAGGIAVNCLGHCHPALVGALKEQGEKIWHLA-NVMTNEPALAL 88

Query: 81  MEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG------ATGKRAIIAFDGGFHGRTL 134
             +L   V  ++       NSGAEA E ALK+AR          K  IIAFD  FHGRT 
Sbjct: 89  ATKL---VEATFAEKVYFANSGAEANEAALKLARRYALDKFGAEKDQIIAFDKAFHGRTF 145

Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVED-VAA 193
            T+++ G+ A Y    G  P  + HLP+                + + ++E  V D   A
Sbjct: 146 FTVSVGGQAA-YSDGFGPKPQSITHLPF----------------NDIAALEAEVSDKTCA 188

Query: 194 FIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPD 253
            + EP+QGEGG +  DP F +A+R   D+   L+I DE+Q+G GR G+ +A+ R  + PD
Sbjct: 189 IMLEPLQGEGGIIDADPEFLRAVRALADKHNALVIFDEVQTGVGRLGELYAYMRTEVTPD 248

Query: 254 LLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLAT 313
           +L  AK++ GG P+ A++   E+ + L  G  G TY GNP++CA   A L  +    +  
Sbjct: 249 ILTTAKALGGGFPIAAMLTTTEIASHLKIGTHGSTYGGNPLACAIGNAVLDVVNTPEVLD 308

Query: 314 WGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAARA 373
             +R+EQ +     R   + ++      T V   +G+            +    + A  +
Sbjct: 309 GVKRREQLL-----RDGLNQINEKYHVFTEVRG-QGLLLGAVLNEQYQGRSKDFLVAGTS 362

Query: 374 RGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
            GL+ + +G   ++IR    L I    + EGL   E+ +A++
Sbjct: 363 EGLMCLIAGP--NVIRFTPSLVIPEADIAEGLARFERAVAKV 402


Lambda     K      H
   0.320    0.137    0.402 

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: 417
Number of extensions: 21
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: 416
Length of database: 405
Length adjustment: 31
Effective length of query: 385
Effective length of database: 374
Effective search space:   143990
Effective search space used:   143990
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: 50 (23.9 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