Alignments for a candidate for glcF in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcF in Dechlorosoma suillum PS

Align D-lactate oxidase and glycolate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate Dsui_3413 Dsui_3413 Fe-S oxidoreductase

Query= reanno::psRCH2:GFF3770
         (405 letters)



>FitnessBrowser__PS:Dsui_3413
          Length = 420

 Score =  523 bits (1347), Expect = e-153
 Identities = 256/417 (61%), Positives = 311/417 (74%), Gaps = 13/417 (3%)

Query: 1   MQTNLSEAAKKLPRAEEAESILRSCVHCGFCNATCPTYQLLGDELDGPRGRIYLMKQMFE 60
           MQT L++  K  P  +EA++ILR+CVHCGFC ATCPTYQLLGDELDGPRGRIYL+KQ+ E
Sbjct: 1   MQTQLADFIKDTPAGKEADAILRTCVHCGFCTATCPTYQLLGDELDGPRGRIYLIKQVLE 60

Query: 61  GGEVTESTQLHLDRCLTCRNCETTCPSGVKYHNLLDIGRDFIEQQVQRPLGERVVRGGLR 120
           GG VTE T+LHLDRCLTCR+CETTCPSGVKYH LLDIGR  +E++V R   E + R  L+
Sbjct: 61  GGPVTERTRLHLDRCLTCRSCETTCPSGVKYHRLLDIGRQVVEERVPRGGLEALTRLALK 120

Query: 121 TVIPRPGLFKALLGAGNALKPLMPASLKDHLPREI-RPAKPRPQVMHSRRVLILEGCVQP 179
            V+PRP LF   +  G  LKP +P+ L D +P     PAKPRP  +  R+VL L GCVQP
Sbjct: 121 EVLPRPWLFNPAVAVGKVLKPFLPSVLGDKIPAAAGGPAKPRPTAVRQRKVLALAGCVQP 180

Query: 180 SLSPSTNAAAARVLDRLGISVSPAREAGCCGAVDYHLNAQDAGLDRARRNIDAWWPAIEA 239
            L+P+ NAAAARVLDRLGI +    +AGCCGA+ +HLNAQ+A LD  RRNIDAWWP +EA
Sbjct: 181 GLAPNINAAAARVLDRLGIQMIEEEKAGCCGALRFHLNAQEAALDDMRRNIDAWWPHVEA 240

Query: 240 GAEAIVQTASGCGAFVKEYGHLLKDDPAYAAKAARVSELAKDLVEVLRSAELEKLNVRAD 299
           GAEAI+ TASGCGA VKEYGHLL+DDPAYAAKAAR++EL KD  E++ + +   L + A 
Sbjct: 241 GAEAILMTASGCGAHVKEYGHLLQDDPAYAAKAARIAELTKDAAELVLAQKEALLPLLAH 300

Query: 300 K-----RMAFHCPCTLQHAQKLGGAVEDVLTRLGYQLTAVPDAHLCCGSAGSYSITQPEI 354
           K     ++AFH PCTLQH Q + G VE++L   G+ LT V D+HLCCGSAG+YSI QPE+
Sbjct: 301 KPAAGRKVAFHSPCTLQHGQGIRGVVEELLAAAGFTLTPVADSHLCCGSAGTYSILQPEL 360

Query: 355 SHQLRDNKLNALESGKPEVIVTANIGCQTHLDGAG-------RTPVKHWIEVVEESM 404
           S QLRDNKL+AL +G PEVI TANIGC THL   G         PV+HW+E++EE +
Sbjct: 361 SKQLRDNKLSALGAGLPEVIATANIGCLTHLQSGGAPRGTPSAVPVRHWVELLEEQL 417


Lambda     K      H
   0.319    0.135    0.410 

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: 650
Number of extensions: 35
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: 405
Length of database: 420
Length adjustment: 31
Effective length of query: 374
Effective length of database: 389
Effective search space:   145486
Effective search space used:   145486
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 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources