GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araA in Megamonas funiformis YIT 11815

Align L-arabinose isomerase (EC 5.3.1.4) (characterized)
to candidate WP_008539391.1 HMPREF9454_RS09240 L-arabinose isomerase

Query= BRENDA::Q2VMT2
         (497 letters)



>NCBI__GCF_000245775.1:WP_008539391.1
          Length = 494

 Score =  573 bits (1477), Expect = e-168
 Identities = 284/498 (57%), Positives = 358/498 (71%), Gaps = 10/498 (2%)

Query: 2   MLSLRPYEFWFVTGSQHLYGEEALKQVEEHSMMIVNELNQDSVFPFPLVFKSVVTTPEEI 61
           M  L+ Y+FWF+ GSQ LYG EALK VEE +  +V  LN     P  + FK+V TT E I
Sbjct: 1   MKKLQDYKFWFIVGSQFLYGPEALKAVEEDAKKMVEGLNASGKLPAKIEFKAVGTTAEVI 60

Query: 62  RRVCLEANASEQCAGVITWMHTFSPAKMWIGGLLELRKPLLHLHTQFNRDIPWDSIDMDF 121
            R  ++AN  + CAG+ITWMHTFSP+KMWI GL +L+KP LHLHTQ+NR+IP + IDMDF
Sbjct: 61  DRFVMDANYDDTCAGIITWMHTFSPSKMWIRGLKKLQKPYLHLHTQYNREIPNEEIDMDF 120

Query: 122 MNLNQSAHGDREYGFIGARMGVARKVVVGHWEDPSVRERLAKWMRTAVAFAESRHLKVAR 181
           MNLNQSAHGDRE+GFIG RM +ARK+VVG+WE  +V+ ++A WMRTA+    S  LKV R
Sbjct: 121 MNLNQSAHGDREHGFIGTRMRLARKIVVGYWETEAVQNKIATWMRTAIGVIASADLKVIR 180

Query: 182 FGDNMREVAVTEGDKVGAQIQFGWSVNGYGVGDLVQYIRDVSEQKINELLEEYAELYDIV 241
           FGDNMR VAVTEGDKV A+I+FGWSVN + VGDLVQYI  V+E++I+  + EY   Y++ 
Sbjct: 181 FGDNMRNVAVTEGDKVEAEIKFGWSVNTHAVGDLVQYINAVTEEQIDAQVAEYQTKYEM- 239

Query: 242 PAGRQDGPVRESIREQARIELGLKAFLKDGNFAAFTTTFEDLHGMKQLPGLAVQRLMAEG 301
                +     S+R QA++E+ +K FL+D     F  TFEDL+GM QLPGLA Q L  +G
Sbjct: 240 -----NTDNIASVRYQAKVEVAIKKFLEDNKADGFVNTFEDLYGMDQLPGLATQDLTGQG 294

Query: 302 YGFGGEGDWKTAALVRLMKVMADG--KGTSFMEDYTYHFEPGNE--MILGAHMLEVCPTI 357
           YGFG EGDWK A L  +MK MA G  KGT+ MEDYTYHF    E    LGAHMLEVCP++
Sbjct: 295 YGFGPEGDWKIACLTAVMKTMAQGVDKGTALMEDYTYHFGKDGEDSYNLGAHMLEVCPSV 354

Query: 358 AATRPRIEVHPLSIGGKEDPARLVFDGGEGAAVNASLIDLGHRFRLIVNEVDAVKPEHDM 417
           A   P+IEVH L IGGK+ PARLVF+G  G A+ A+L+D+G R RLIVN+V+ VKP   M
Sbjct: 355 AEGTPKIEVHELGIGGKDAPARLVFEGKAGGAIVATLVDMGGRMRLIVNDVECVKPIMPM 414

Query: 418 PKLPVARILWKPRPSLRDSAEAWILAGGAHHTCFSFAVTTEQLQDFAEMAGIECVVINEH 477
           P LPVAR++WKP PSL ++ EAWILAGGAHH+  S+ VT EQL+D+A M GIE V I + 
Sbjct: 415 PNLPVARVMWKPMPSLEEAGEAWILAGGAHHSVISYTVTAEQLRDWANMMGIEFVHITKD 474

Query: 478 TSVSSFKNELRWNEVFWR 495
             +  FK++L  +++ W+
Sbjct: 475 LDMDKFKDQLMLSDIMWK 492


Lambda     K      H
   0.321    0.137    0.423 

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: 698
Number of extensions: 31
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: 497
Length of database: 494
Length adjustment: 34
Effective length of query: 463
Effective length of database: 460
Effective search space:   212980
Effective search space used:   212980
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 (21.9 bits)
S2: 52 (24.6 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