Alignments for a candidate for glcB in Erythrobacter gangjinensis K7-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for glcB in Erythrobacter gangjinensis K7-2

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate WP_071961211.1 AAW01_RS03850 malate synthase G

Query= reanno::psRCH2:GFF353
         (726 letters)



>NCBI__GCF_001010925.1:WP_071961211.1
          Length = 715

 Score =  777 bits (2007), Expect = 0.0
 Identities = 407/722 (56%), Positives = 503/722 (69%), Gaps = 29/722 (4%)

Query: 5   VQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDLQAQI 64
           VQ  GL V  VL  FV  EA+PGTGV A AFW G  ++  +  P+NRALL  R  LQA I
Sbjct: 22  VQRAGLAVDPVLAAFVETEALPGTGVSADAFWQGLANLAGEFTPRNRALLEARARLQAMI 81

Query: 65  DAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVPIMNA 124
           D WH+     A   +  +  L+ +GYL+ E   F   TEN D+EIA +AGPQLVVP  NA
Sbjct: 82  DQWHRDNP-DAGTGMPPRD-LKALGYLVEEPAPFTIGTENTDDEIALLAGPQLVVPARNA 139

Query: 125 RFALNAANARWGSLYDALYGTDAISEADGASKGPG-YNEIRGNKVIAYARNFLNEAAPLE 183
           RF LNA NARWGSLYDALYGTDA+   DG+    G YN+ RG KV+A+A+ FL++A PL 
Sbjct: 140 RFVLNAVNARWGSLYDALYGTDAL---DGSLPEKGDYNQTRGAKVVAWAKAFLDDAVPLA 196

Query: 184 TGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHFEIQ 243
            GS  + TG                T  L +PAQ  G       P+ V   NNG+  E+ 
Sbjct: 197 NGSWSEWTG---------------GTPELSDPAQFIGMAD--GNPVLV---NNGLKIELV 236

Query: 244 IDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDLVEE 303
           I+   PIG+ D A + DI +ESAL+TI+D EDS+AAVD +DK   YRNWLG ++GDL   
Sbjct: 237 INADHPIGRDDPASIADIRLESALSTIIDLEDSVAAVDGEDKADGYRNWLGALRGDLEAT 296

Query: 304 LEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEVPEG 363
             KGG+ + R  NPDR YT ADG  +  L  RSLL +RNVGHLMT  A+   +G+E+ EG
Sbjct: 297 FIKGGRTMKRVANPDRTYTAADGETK-PLRTRSLLLVRNVGHLMTTPAVSLPDGSEMFEG 355

Query: 364 IMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLGLPR 423
           ++D   TSLI +H+LN      N+  G +YIVKPKMHGPEE AFA +LF  VED+LGL R
Sbjct: 356 LLDAATTSLIGLHDLNRLGPLANSAEGRIYIVKPKMHGPEECAFADDLFAAVEDMLGLAR 415

Query: 424 NTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKAAMK 483
           NT+K+G+MDEERRT+ NL ACI   R+R+ FINTGFLDRTGDEIHTSM AGPM+RK A+K
Sbjct: 416 NTIKIGVMDEERRTSANLAACIHAVRDRIFFINTGFLDRTGDEIHTSMLAGPMMRKGAIK 475

Query: 484 AEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAWVPS 543
             +WI+AYE+ NV +GLACG  G+AQIGKGMWA PD M  MLEQK+GHPM+GA+TAWVPS
Sbjct: 476 QAEWIAAYEDRNVQIGLACGFAGRAQIGKGMWAAPDAMHDMLEQKIGHPMSGASTAWVPS 535

Query: 544 PTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNELDNNSQG 603
           PTAATLHA HYH+  V  RQ E A+     +D +LT+PLA+D +W+E+E   ELDNN QG
Sbjct: 536 PTAATLHATHYHRCTVSERQSERAQERIVPVDKLLTVPLAEDADWTEDEIAAELDNNVQG 595

Query: 604 ILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVESLKR 663
           ILGYMVRW++ GVGCSKVPDI+D+ LMEDRATLRISSQH+ANW++HG+V +  + E+L R
Sbjct: 596 ILGYMVRWIDAGVGCSKVPDIHDVGLMEDRATLRISSQHIANWLQHGIVDRLMIDEALHR 655

Query: 664 MAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREFKAK 723
           MA  VD QN GDP YRPM+ D   S+A  AA +L++ G KQP+GYTEPVLHR R   +AK
Sbjct: 656 MAAKVDAQNAGDPDYRPMSADERGSIAMAAARKLIVAGAKQPSGYTEPVLHRAR--LRAK 713

Query: 724 NG 725
           +G
Sbjct: 714 HG 715


Lambda     K      H
   0.316    0.133    0.386 

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: 1460
Number of extensions: 60
Number of successful extensions: 5
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: 726
Length of database: 715
Length adjustment: 40
Effective length of query: 686
Effective length of database: 675
Effective search space:   463050
Effective search space used:   463050
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: 55 (25.8 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:

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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