GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Amycolatopsis halophila YIM 93223

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein

Query= reanno::psRCH2:GFF2388
         (503 letters)



>NCBI__GCF_000504245.1:WP_034273599.1
          Length = 496

 Score =  254 bits (649), Expect = 5e-72
 Identities = 162/487 (33%), Positives = 255/487 (52%), Gaps = 11/487 (2%)

Query: 11  KLLIDGEFIEST-TQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAF--KTWRKTP 67
           +L IDG ++++T T   R V+NPA    LA V  A  +++D AVA+ ++AF    WR T 
Sbjct: 3   ELFIDGRWVDTTGTAPARVVLNPANAAELATVCEADEKDVDAAVAAARRAFDDSPWRATT 62

Query: 68  IGARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAGIGNLQLG 127
              R  +  +  +L++ + + LA   + + GKT+A+   DV     V  + A + + + G
Sbjct: 63  ARERGELLREIARLLQRDKEHLARTESLDTGKTMAEGRVDVDDVTSVFRYYANLADNEAG 122

Query: 128 ELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 187
            + +   A V +  + +P+GVC+ I P+N+P +   W    A+A GNT V+KPSE  P+ 
Sbjct: 123 RVVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTPLT 182

Query: 188 TMRLCELALEAGVPPGVLNVVHGGPDVVNA-ICDHPDIKAVSFVGSTKVGTHVYNRASQA 246
           T+ L  L  EAGVP GV+N+V GG   V A +  HPD+  VSF G  + G  +   A++ 
Sbjct: 183 TIELMRLVEEAGVPAGVVNLVLGGGANVGAPMVSHPDVDLVSFTGGLETGKKIMAMAAEG 242

Query: 247 GKRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEA-QAWIPD 305
            KRV   +G KN  +V  DA  +  ++    AAF  +GQ C A S +++  +    ++ +
Sbjct: 243 VKRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEFVAE 302

Query: 306 LVAKAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSGYEN 365
           L  +A  +++  G++  T+ GPL S    D+V   IE    EGA+L + G  P+     +
Sbjct: 303 LARRADAIRLGDGLDPATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPTEPELAD 362

Query: 366 GNFVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIFTRSGA 425
           G F+ PT+F+   REM + Q+E+FGPV+ V    T DEAI L N    G   A++T   +
Sbjct: 363 GYFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWTSDAS 422

Query: 426 AARHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLG-DLGPYG----KQVVQFYTQTK 480
            A+     +  G V IN   P  +P   + G   S +G +LGP G    ++    Y   +
Sbjct: 423 RAQRVAGALRHGTVWINDFHPY-LPQAEWGGFGKSGIGRELGPSGLEEYRETKHIYQNIR 481

Query: 481 TITERWF 487
               RWF
Sbjct: 482 PAPMRWF 488


Lambda     K      H
   0.318    0.134    0.394 

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: 585
Number of extensions: 26
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: 503
Length of database: 496
Length adjustment: 34
Effective length of query: 469
Effective length of database: 462
Effective search space:   216678
Effective search space used:   216678
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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