Alignments for a candidate for TM0028 in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for TM0028 in Halomonas desiderata SP1

Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate WP_086508118.1 BZY95_RS00870 ABC transporter ATP-binding protein

Query= TCDB::Q9WXN5
         (330 letters)



>NCBI__GCF_002151265.1:WP_086508118.1
          Length = 766

 Score =  238 bits (607), Expect = 4e-67
 Identities = 134/320 (41%), Positives = 198/320 (61%), Gaps = 11/320 (3%)

Query: 5   LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT 64
           LLK E++  +Y+     V+AVDG+ F++   E +G+VGESGCGKTT +  + + ++ P  
Sbjct: 6   LLKVEDLAIHYRTGAGPVQAVDGIHFDLRPGEALGLVGESGCGKTTAAKAM-LRLLPP-- 62

Query: 65  LVDGKIFL-RVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLA 123
             +G++   R++ +  +L ++  + +++  W KEI  I QAAMNAL P   +   +    
Sbjct: 63  --NGEVPRGRIDFDGRDLVALDEESMRKVRW-KEIAWISQAAMNALDPVYTVGDQILEAM 119

Query: 124 ESH-GIDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIAD 182
            +H  ID +     A   F  VG+DP  +  YP E+SGGM+QRAVIA+A  L+P L+IAD
Sbjct: 120 NAHIKIDRKTAWAHAEELFRAVGIDPGRLSAYPHEMSGGMKQRAVIAMALALDPKLIIAD 179

Query: 183 EPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAP 242
           EPT+ALDVV Q  +L  L +++R+  +  ++FITHDI+ V Q  DR+ +MY G I+E  P
Sbjct: 180 EPTTALDVVTQAQILARLSKLRRERGM-GLLFITHDISVVVQTCDRVAVMYGGHIMETGP 238

Query: 243 VESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMD 302
           V  +   P HPYT GL N+   P  E  +R + +IPG+PP+L+NPPSGCRF  RCP A +
Sbjct: 239 VREVFGTPFHPYTMGLTNAF--PTLEGAQRELISIPGSPPDLLNPPSGCRFAERCPFATE 296

Query: 303 VCKEKEPPLTEIEPGRRVAC 322
            C  + PPL  +   R+ AC
Sbjct: 297 RCVRETPPLHPVGEERQAAC 316



 Score =  175 bits (443), Expect = 4e-48
 Identities = 112/316 (35%), Positives = 170/316 (53%), Gaps = 27/316 (8%)

Query: 4   ILLKAENVRAYYKLEKV------------SVKAVDGLSFEILEDEVIGVVGESGCGKTTL 51
           +LL+ E ++ ++ +E+              V AVDG+SF++ E E++G+ GESG GKTT 
Sbjct: 361 LLLEVEELKKHFPVEQGFLDGLRGRNKDRKVHAVDGISFDLREGEILGLAGESGSGKTTT 420

Query: 52  SNVIFMNMVKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMP 111
             ++    V+ L + +G+I      E  +++ +T  E+K   + +   +I Q     L P
Sbjct: 421 GEML----VRLLDVTEGEIRF----EGADIAQLTGRELKT--FRRRAQMIFQDPYQTLNP 470

Query: 112 TIRMEKYVRHLAESHGIDEEELL-DKARRRFEEVGLDP--LWIKRYPFELSGGMRQRAVI 168
              +   V      H + E E L  K     E  GL P  ++ +R+P ELSGG RQR  I
Sbjct: 471 RFTIFDIVAEPLIIHRLAEGEALRQKVVVALERAGLKPAEVYAERFPHELSGGQRQRVAI 530

Query: 169 AIATILNPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADR 228
           A A +L P  ++ADEP S LDV  +  +L  LM   R  +  S ++++HD+ T+R +ADR
Sbjct: 531 ARAIVLEPRFIVADEPVSMLDVSIRAGVLN-LMHRFRNELGISFVYVSHDLPTIRYVADR 589

Query: 229 MIIMYAGKIVEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPP 288
             IMY G+IVE  P E ++ +  HPYTQ L  +   P+P V K  + +  G  P+ + PP
Sbjct: 590 TAIMYLGEIVEVGPTEQVVRERKHPYTQLLLEASPEPDPAVVKPPLES-AGEIPSAVEPP 648

Query: 289 SGCRFHPRCPHAMDVC 304
           +GC FH RCP AM  C
Sbjct: 649 NGCHFHTRCPRAMAHC 664


Lambda     K      H
   0.321    0.138    0.405 

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: 663
Number of extensions: 38
Number of successful extensions: 9
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: 330
Length of database: 766
Length adjustment: 34
Effective length of query: 296
Effective length of database: 732
Effective search space:   216672
Effective search space used:   216672
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: 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