GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Pedobacter sp. GW460-11-11-14-LB5

Align aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate CA265_RS07515 CA265_RS07515 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::Q9SIE1
         (475 letters)



>FitnessBrowser__Pedo557:CA265_RS07515
          Length = 380

 Score =  339 bits (869), Expect = 1e-97
 Identities = 183/383 (47%), Positives = 241/383 (62%), Gaps = 4/383 (1%)

Query: 87  ITDLAATLVQSGVPVIRLAAGEPDFDTPKVVAEAGINAIREGFTRYTLNAGITELREAIC 146
           +T L   L   G+ +I L+ GEPDF+TP  V  A   A+ E +TRY+   G  +LR+AI 
Sbjct: 1   MTKLGRELASKGINIISLSVGEPDFNTPDHVKNAAKKALDENYTRYSPVPGYPDLRQAIV 60

Query: 147 RKLKEENGLSYAPDQILVSNGAKQSLLQAVLAVCSPGDEVIIPAPYWVSYTEQARLADAT 206
            KLK EN L Y   QI+VS GAKQSL   +L +  P DEVIIP PYWVSY+E   LA+  
Sbjct: 61  NKLKTENNLDYDISQIVVSTGAKQSLSNVILTLIDPDDEVIIPTPYWVSYSEMVTLAEGK 120

Query: 207 PVVIPTKISNNFLLDPKDLESKLTEKSRLLILCSPSNPTGSVYPKSLLEEIARIIAKHPR 266
            V I T I ++F + P  LE+ +T KS+L +  SP NPTGSVY K  L  +  +  KHP 
Sbjct: 121 SVFIDTDIESDFKITPAQLEAAITPKSKLFMFSSPCNPTGSVYSKEELAALVAVFEKHPN 180

Query: 267 LLVLSDEIYEHIIYAPATHTSFASLPDMYERTLTVNGFSKAFAMTGWRLGYLAGPKHIVA 326
           + +LSDEIYEHI +    H S A    + +R + VNGFSKAFAMTGWRLGY+A  K I A
Sbjct: 181 IYILSDEIYEHINFVD-KHESIAQFDSIKDRVIIVNGFSKAFAMTGWRLGYIAANKEIAA 239

Query: 327 ACSKLQGQVSSGASSIAQKAGVAALGLGKAGGETVAEMVKAYRERRDFLVKSLGDIKGVK 386
           A  KLQGQ +SG  SIAQ+AG+ A   G A   +V EM +A+  RR+ +   L +I GVK
Sbjct: 240 ANDKLQGQTTSGTCSIAQRAGIVAYEQGLA---SVLEMKEAFLRRRELVYNLLNEIPGVK 296

Query: 387 ISEPQGAFYLFIDFSAYYGSEAEGFGLINDSSSLALYFLDKFQVAMVPGDAFGDDSCIRI 446
            + P GAFY F + S+++G +     +I DSS LALY L+   VA V GD+FG+++ IR+
Sbjct: 297 TNLPDGAFYFFPEISSFFGKKDADGNVIKDSSDLALYLLNVGHVATVGGDSFGNNNYIRL 356

Query: 447 SYATSLDVLQAAVEKIRKALEPL 469
           SYA S + L  A+ +I++AL  L
Sbjct: 357 SYAASDESLVEALRRIKEALGKL 379


Lambda     K      H
   0.317    0.132    0.370 

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: 404
Number of extensions: 15
Number of successful extensions: 3
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: 475
Length of database: 380
Length adjustment: 32
Effective length of query: 443
Effective length of database: 348
Effective search space:   154164
Effective search space used:   154164
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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