GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ARO8 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)



>lcl|FitnessBrowser__Pedo557:CA265_RS07515 CA265_RS07515 pyridoxal
           phosphate-dependent aminotransferase
          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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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