GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Hafnia paralvei ATCC 29927

Align D-galactosamine-6-phosphate deaminase AgaS; GalN-6-P deaminase; Glucosamine-6-phosphate deaminase; GlcN-6-P deaminase; EC 3.5.99.-; EC 3.5.99.6 (characterized)
to candidate WP_064575374.1 M988_RS19180 hypothetical protein

Query= SwissProt::A0KYQ7
         (386 letters)



>NCBI__GCF_001655005.1:WP_064575374.1
          Length = 392

 Score =  174 bits (442), Expect = 3e-48
 Identities = 127/390 (32%), Positives = 195/390 (50%), Gaps = 26/390 (6%)

Query: 14  SNLLLSAEQLTQYGAFWTAKEISQQPKMWRKVSEQHSDNRTIAAWLTPILAKPQLRIILT 73
           SN L S  +    G   T + I  QP++WR+       +R         LA     IIL 
Sbjct: 5   SNTLFSEAEWQSAGGLLTLQSICNQPRLWREGFALIQQHRAEIRRFWQQLADEPRNIILC 64

Query: 74  GAGTSAYIGDVLAAHIQQHLPLATQQVEAISTTDIVSHPELYLRGNIPTLLISYGRSGNS 133
           GAG+S     V A  I+Q      + ++ +++TDIV  PELYL  N PTLL+S   SG++
Sbjct: 65  GAGSSLSAARVAAQWIRQQ---TGKSIQVLASTDIVVKPELYLE-NKPTLLVSVTSSGST 120

Query: 134 PESMAAVELAEQLVDDCYHLAITCNGQGKLANYCADKSHCYLYKLPDETHDVSFAMTSSF 193
           PES A  ELAE+L+DDCYHL +  + QG+L       +       P  T + SFA  + F
Sbjct: 121 PESTAVFELAERLIDDCYHLIVANDPQGELPKRSQHHAKTLYIPAPIGTKNGSFAAAAEF 180

Query: 194 TCMYLATLLIFAPN-----SQALMQCIEMAEHILTERLADIRLQSEQPSKRVVFLGGGPL 248
           T      LLIF P       +AL      A++ L+++   I   +++ +  VV LG   L
Sbjct: 181 TLPIWYLLLIFLPQQWDIAQRALDVYQHGADYFLSQQADKIAAIAKRDAPMVVSLGSSSL 240

Query: 249 KAIAQEAALKYLELTAGQVVSAFESPLGFRHGPKSLVDSHTQVLVMMSSDPYTRQYDNDL 308
           + IA +A+LK LE+  G+  +   S L FRHGPK +V+    V+  +S D    +YD D+
Sbjct: 241 QFIAADASLKLLEMCNGRQATDDFSTLAFRHGPKLIVNQPVTVVCYLSPDQEILRYDLDM 300

Query: 309 IQELKR----DNQALSVLTLSEELLTGS------------SGLNEVWLGLPFILWCQILA 352
             EL        + + +   ++E +  +            + L EV+ GL ++++ Q+L 
Sbjct: 301 ATELAAQRHPQGKIIGIYAANDERVAQACDEYLHFDSPELTQLPEVFSGLLYVMFAQLLG 360

Query: 353 IYKAIQLKVSPDNPCPTGQVNRVVQGVNVY 382
           + +A QL V+PD P   G+V +V + V +Y
Sbjct: 361 LLRARQLGVTPDLPSNDGKVAKVCK-VTIY 389


Lambda     K      H
   0.319    0.133    0.392 

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: 327
Number of extensions: 18
Number of successful extensions: 6
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: 386
Length of database: 392
Length adjustment: 30
Effective length of query: 356
Effective length of database: 362
Effective search space:   128872
Effective search space used:   128872
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 24 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