Alignments for a candidate for TM0028 in Halococcus hamelinensis 100A6

GapMind for catabolism of small carbon sources

Alignments for a candidate for TM0028 in Halococcus hamelinensis 100A6

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_007694542.1 C447_RS12845 ABC transporter ATP-binding protein

Query= TCDB::Q9WXN5
         (330 letters)



>NCBI__GCF_000336675.1:WP_007694542.1
          Length = 732

 Score =  197 bits (501), Expect = 7e-55
 Identities = 110/308 (35%), Positives = 184/308 (59%), Gaps = 7/308 (2%)

Query: 25  VDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVELSSM 84
           ++ ++  I   EV+G+VGESG GK+  ++ +   +  P  L     +   +G  V++  +
Sbjct: 38  LEDVNVNIDRHEVLGIVGESGSGKSMFASALLDAVPDPGKLSGQIQYHGQDGSTVDILEL 97

Query: 85  TRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHGIDEEELLDKARRRFEEV 144
           + +E+++  W +E++++ Q AM++  PT+++  + +    +H  D  + LD AR   E +
Sbjct: 98  SDEELRQFRW-EEVSMVFQGAMSSFNPTMKIGGHFKETLRTHDRDVSKGLDFARELLENL 156

Query: 145 GLDPLWI-KRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLKVLMQM 203
            L+P  +   YP ELSGGM+QRA+IA++  LNP +L+ DEPT+ALD++ Q+ +L++L  +
Sbjct: 157 YLEPERVLDSYPHELSGGMQQRALIALSMALNPEVLVMDEPTAALDLLMQRSILQLLDDL 216

Query: 204 KRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQGLFNSVL 263
           + +  + +I+FITHD+  V  +ADRM I+YA +  E  P + ++    HPYT+ L N+  
Sbjct: 217 QSEYDL-TIVFITHDLPLVASLADRMAIIYAFQFAEIGPRDEIIGNSAHPYTRALLNA-- 273

Query: 264 TPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMDVCKEKEPPLTEIEPG--RRVA 321
           TP  +     +  I G  P  +N PSGCRFHPRCP A + C+  EPPL  ++ G   R A
Sbjct: 274 TPNLDAPLSEMEPIEGEGPAPVNIPSGCRFHPRCPLATEKCQRDEPPLAAVDGGTEHRAA 333

Query: 322 CWLYMEER 329
           C  + E R
Sbjct: 334 CHYHDEAR 341



 Score =  161 bits (407), Expect = 5e-44
 Identities = 113/345 (32%), Positives = 184/345 (53%), Gaps = 35/345 (10%)

Query: 3   EILLKAENVRAYYK-----LEKVS-----VKAVDGLSFEILEDEVIGVVGESGCGKTTLS 52
           E LL  ++V  ++      LE+ S     V+AVDG+S +I E +++ ++GESGCGKTTL 
Sbjct: 373 EPLLSLDDVEVHFTKEQGLLERFSGDPEVVRAVDGVSLDIEEQDLVCLLGESGCGKTTLG 432

Query: 53  NVIFMNMVKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPT 112
             + + + +P     G I     G+ +  +  +  +V        + II Q   +AL P 
Sbjct: 433 KTM-IGLQRP---TGGSI--EYQGQDIWEADESDSDVSYDDIRSALQIIHQDPGSALNPN 486

Query: 113 IRMEKYV----RHLAESHGIDEEELLDKARRRFEEVGLDPL--WIKRYPFELSGGMRQRA 166
            R+   +    RH   + G +E     +     E VG+ P   ++ RYP +LSGG +QR 
Sbjct: 487 RRIANILAEPLRHTYPNIGRNERR--SRMHSLLERVGMTPAGDFLDRYPHQLSGGEKQRV 544

Query: 167 VIAIATILNPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIA 226
           V+A A ++NP  ++ADE  SA+DV  +  ++ ++++++      S +FI+HD++  R  A
Sbjct: 545 VLARALLMNPDAILADEAISAVDVSLRIEIMDLMLELQSD-FNTSFLFISHDLSNARYFA 603

Query: 227 D----RMIIMYAGKIVEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAP- 281
           +    R+ +MY G+IVE    E L+  P HPYT+ L     TP+ ++   G    P    
Sbjct: 604 EHGDGRIAVMYLGEIVEIGSAERLIHDPRHPYTEVL--RWATPDLDLDAMGADDPPIREI 661

Query: 282 --PNLINPPSGCRFHPRCPHAMDVCKEKEPPLTEIE-PGRRVACW 323
             P+ ++PPSGCRFH RCP A + C+E+ P L ++E  G   AC+
Sbjct: 662 DVPDPVDPPSGCRFHTRCPVARETCREQHPDLLDVEGAGGSAACF 706


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: 43
Number of successful extensions: 11
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: 732
Length adjustment: 34
Effective length of query: 296
Effective length of database: 698
Effective search space:   206608
Effective search space used:   206608
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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Protein sequences (fasta format)
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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