Alignments for a candidate for SLC13A5 in Erythrobacter marinus HWDM-33

GapMind for catabolism of small carbon sources

Alignments for a candidate for SLC13A5 in Erythrobacter marinus HWDM-33

Align Solute carrier family 13 member 2 (Na /di- and tricarboxylate cotransporter 1) (NaDC-1) (Renal sodium/dicarboxylate cotransporter) (characterized)
to candidate WP_047094455.1 AAV99_RS12860 C4-dicarboxylate ABC transporter

Query= TCDB::Q13183
         (592 letters)



>NCBI__GCF_001013305.1:WP_047094455.1
          Length = 502

 Score =  219 bits (559), Expect = 2e-61
 Identities = 168/542 (30%), Positives = 258/542 (47%), Gaps = 75/542 (13%)

Query: 19  FVPILLLPLPILVPSKEAYCAYAIILMALFWCTEALPLAVTALFPLILFPMMGIVDASEV 78
           F   LLLP P  +       A  ++ MA +W T+A+PL  T L P  + P +    A+EV
Sbjct: 15  FALTLLLPAPAGMIGPAWNTAGLVMWMATWWMTQAIPLTATGLLPFAVLPFVSAGTANEV 74

Query: 79  AVEYLKDSNLLFFGGLLVAIAVEHWNLHKRIALRVLLIVGVRPAP--LILGFMLVTAFLS 136
           A +Y      L  GG  +A+A+E   LHKR+A  +L  +G R     L+LGFM+  A LS
Sbjct: 75  AGDYYSPIIFLLLGGAFLALAIERTGLHKRLACWILDRIGGRGGEFGLLLGFMIAAAILS 134

Query: 137 MWISNTATSAMMVPIAHAVLDQLHSSQASSNVEEGSNNPTFELQEPSPQKEVTKLDNGQA 196
             ISNT+T+ +M+P+A AVL       ASS  E      +    E   QKE         
Sbjct: 135 NIISNTSTALIMMPMALAVLS---GGAASSCNEVIGQKGSTSCNEVIGQKE--------- 182

Query: 197 LPVTSASSEGRAHLSQKHLHLTQCMSLCVCYSASIGGIATLTGTAPNLVLQGQINSLFPQ 256
                     RA  +     L+  + + + ++ASIGG+ T+ G+  N +    +  +   
Sbjct: 183 ---------SRADGTLDQSGLSGALPMGLAFAASIGGLGTIIGSPTNAIGVALLRDI--- 230

Query: 257 NGNVVNFASWFSFAFPTMVILLLLAWLWLQILFLGFNFRKNFGIGEKMQEQQQAAYCVIQ 316
           +G  + FA W  F  P ++  + LA +                I  K+Q      + +  
Sbjct: 231 SGIEITFAQWAMFGVPIVIAGIPLAAV----------------IIAKVQRIADHPFDLSA 274

Query: 317 TEHRLL--GPMTFAEKAISILFVILVLLWFTREPGFFLGWGNLAFPNAKGESMVSDGTVA 374
               +   GP + AE+ +  +  +  L W  R  GF   +    FP    E  ++DGTVA
Sbjct: 275 ARKAIAPQGPWSEAERRLVPVIAVTFLAWMLR--GFVAPY----FP----EGSLTDGTVA 324

Query: 375 IFIGIIMFIIPSKFPGLTQDPENPGKLKAPLGLLDWKTVNQKMPWNIVLLLGGGYALAKG 434
           I    ++F +P          +  G+      LL+W+  N + PW+++++ GGG ALA  
Sbjct: 325 IAAAFLLFTLP----------DGTGRR-----LLEWREAN-RAPWDVLMMFGGGLALAGA 368

Query: 435 SERSGLSEWLGNKLTPLQSVPAPAIAIILSLLVATFTECTSNVATTTIFLPILASMAQAI 494
             R+GL++WLGN L PL  VP   IA+ L  +V   TE  SNVAT +  +P++A++A AI
Sbjct: 369 MTRTGLADWLGNALLPLAGVPVIVIALALVAMVILITEFASNVATASGIMPVVAALAVAI 428

Query: 495 CLHP-----LYVMLPCTLATSLAFMLPVATPPNAIVFSFGDLKVLDMARAGFLLNIIGVL 549
                    L + +P  LA S  F+LP  T PNAI +S G + +  + +AG  L+I G+ 
Sbjct: 429 SGESGGNVVLLLAMPVALAASWGFVLPAGTGPNAIAWSTGRIALPRLIKAGITLDIAGIF 488

Query: 550 II 551
           +I
Sbjct: 489 LI 490


Lambda     K      H
   0.325    0.138    0.429 

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: 790
Number of extensions: 41
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 592
Length of database: 502
Length adjustment: 35
Effective length of query: 557
Effective length of database: 467
Effective search space:   260119
Effective search space used:   260119
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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
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