GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lysN in Magnetospirillum magneticum AMB-1

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_083763404.1 AMB_RS01605 aspartate aminotransferase family protein

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



>lcl|NCBI__GCF_000009985.1:WP_083763404.1 AMB_RS01605 aspartate
           aminotransferase family protein
          Length = 384

 Score =  184 bits (468), Expect = 3e-51
 Identities = 132/408 (32%), Positives = 204/408 (50%), Gaps = 41/408 (10%)

Query: 16  ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA--FNAAP 73
           +    G  A ++  DG+RY+DF  G+ V  LGHC+P +V+A+ AQA ++ H +  +  A 
Sbjct: 9   LAFERGEGAYLFTADGRRYLDFAAGVAVNALGHCHPRLVKALTAQAAKVWHTSNLYRVAG 68

Query: 74  HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDG 127
                A      + V  S+       NSGAEA E ++K+AR      G   +  II  +G
Sbjct: 69  QESVAA------KLVERSFADTVFFCNSGAEALECSIKMARRHHFAAGNPQRYRIICAEG 122

Query: 128 GFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELA 187
            FHGRTLAT+   G+    +     + G   H+PY + +       AL+A          
Sbjct: 123 AFHGRTLATVAAGGQKKHLEGFAPAVDG-FDHVPYGNLN-------ALRAS--------I 166

Query: 188 VEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPR 247
            E+ AA + EPVQGEGG +  DP + + LR   DE G+L+I DE+Q+G GRTG  FA  +
Sbjct: 167 TEETAAILVEPVQGEGGIVPGDPDYLRRLRATADEFGLLLIFDEVQTGMGRTGTLFAHEQ 226

Query: 248 LGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMT 307
            GI PD++ +AK + GG P+GA +   +  + +  G  G T+ GNP++ A A   L  M 
Sbjct: 227 AGIAPDIMGVAKGLGGGFPVGACLATTKAASGMVPGTHGSTFGGNPLAMAVAGEVLDIMA 286

Query: 308 DENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKV 367
           +       +     + S+ E   A+     +  + G+G M GI+       P    +A++
Sbjct: 287 EPGFLEHVQAMAALLRSKVED-TAARFPGVVEEVRGLGLMLGIK----PRMPNTEMVARL 341

Query: 368 MEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
            E     GLL + +G   +I+RLL PL I    ++E + IL +   E+
Sbjct: 342 AEG----GLLTVGAGD--NIVRLLPPLIINDAQVDEAVGILARAFDEV 383


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: 434
Number of extensions: 18
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: 384
Length adjustment: 31
Effective length of query: 385
Effective length of database: 353
Effective search space:   135905
Effective search space used:   135905
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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